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10086 (A > C)

MT-ND1_5xtc_s_j_VA144I_NB10H

General info

Mitimpact ID
MI.15021
Chr
chrM
Start
10086
Ref
A
Alt
C
Gene symbol
MT-ND3 Extended gene annotation
Gene position
28
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
AAC/CAC
AA pos
10
AA ref
N
AA alt
H
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10086A>C
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
1.06 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0.012 Conservation Score
PhastCons 470way
0.004 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Likely benign Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Medium Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Vus- Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
10086A>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
.
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

10086 (A > G)

MT-ND1_5xtc_s_j_VA144G_NB10D MT-ND1_5xtc_s_j_VA305I_NB10D MT-ND1_5xtc_s_j_VA305G_NB10D MT-ND1_5xtc_s_j_VA305F_NB10D MT-ND1_5xtc_s_j_VA305L_NB10D MT-ND1_5xtc_s_j_VA144L_NB10D MT-ND1_5xtc_s_j_VA305A_NB10D MT-ND1_5xtc_s_j_VA144D_NB10D MT-ND1_5xtc_s_j_VA144A_NB10D MT-ND1_5xtc_s_j_VA305D_NB10D MT-ND1_5xtc_s_j_VA144I_NB10D MT-ND1_5xtc_s_j_VA144F_NB10D

General info

Mitimpact ID
MI.15020
Chr
chrM
Start
10086
Ref
A
Alt
G
Gene symbol
MT-ND3 Extended gene annotation
Gene position
28
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
AAC/GAC
AA pos
10
AA ref
N
AA alt
D
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10086A>G
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
1.06 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0.012 Conservation Score
PhastCons 470way
0.004 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging Score and details of the predictor
SIFT
Deleterious Score and details of the predictor
SIFT4G
Tolerated Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Likely benign Score and details of the predictor
CADD
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Medium Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Vus- Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
693260
Clinvar ALLELEID
680150
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
10086A>G
MITOMAP Disease Clinical info
Hypertensive end-stage renal disease
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.7606%
MITOMAP General GenBank Seqs
465
MITOMAP General GenBank Curated refs
11553319 23563965 10739760 11938495 27217714 16865696 12509511 29987491 17617636 11349229 11532685 16172508 12949126
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56433
Gnomad AC hom
1197
Gnomad AF hom
0.021211
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
573
HelixMTdb AF hom
0.0029237
HelixMTdb AC het
4
HelixMTdb AF het
2.04e-05
HelixMTdb mean ARF
0.77078
HelixMTdb max ARF
0.90909
ToMMo JPN54K AC
2
ToMMo JPN54K AF
3.7e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs28358274

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
0.15 CPD variant frequency
AA ref
N
CPD AA alt
D
Aln pos
12
RefSeq protein ID
YP_002004588
Species name
Propithecus coquereli
Ncbi taxon ID
379532

10086 (A > T)

MT-ND1_5xtc_s_j_VA144I_NB10Y

General info

Mitimpact ID
MI.15019
Chr
chrM
Start
10086
Ref
A
Alt
T
Gene symbol
MT-ND3 Extended gene annotation
Gene position
28
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
AAC/TAC
AA pos
10
AA ref
N
AA alt
Y
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10086A>T
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
1.06 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0.012 Conservation Score
PhastCons 470way
0.004 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Tolerated Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Ambiguous Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Medium Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Vus Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
10086A>T
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
.
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

10087 (A > C)

MT-ND1_5xtc_s_j_VA144I_NB10T

General info

Mitimpact ID
MI.15022
Chr
chrM
Start
10087
Ref
A
Alt
C
Gene symbol
MT-ND3 Extended gene annotation
Gene position
29
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
AAC/ACC
AA pos
10
AA ref
N
AA alt
T
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10087A>C
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
2.452 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0.044 Conservation Score
PhastCons 470way
0.004 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Tolerated Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Neutral Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Likely benign Score and details of the predictor
CADD
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Neutral Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Likely-benign Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
10087A>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
.
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

10087 (A > G)

MT-ND1_5xtc_s_j_VA144I_NB10S

General info

Mitimpact ID
MI.15023
Chr
chrM
Start
10087
Ref
A
Alt
G
Gene symbol
MT-ND3 Extended gene annotation
Gene position
29
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
AAC/AGC
AA pos
10
AA ref
N
AA alt
S
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10087A>G
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
2.452 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0.044 Conservation Score
PhastCons 470way
0.004 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Tolerated Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Neutral Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Likely benign Score and details of the predictor
CADD
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Neutral Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Likely-benign Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
10087A>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
.
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

10087 (A > T)

MT-ND1_5xtc_s_j_VA144I_NB10I

General info

Mitimpact ID
MI.15024
Chr
chrM
Start
10087
Ref
A
Alt
T
Gene symbol
MT-ND3 Extended gene annotation
Gene position
29
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
AAC/ATC
AA pos
10
AA ref
N
AA alt
I
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10087A>T
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
2.452 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0.044 Conservation Score
PhastCons 470way
0.004 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Neutral Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Likely benign Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Neutral Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Vus- Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
High impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
10087A>T
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
.
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

10088 (C > A)

MT-ND1_5xtc_s_j_VA144I_NB10K MT-ND1_5xtc_s_j_VA144I_NB10K

General info

Mitimpact ID
MI.15025
Chr
chrM
Start
10088
Ref
C
Alt
A
Gene symbol
MT-ND3 Extended gene annotation
Gene position
30
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
AAC/AAA
AA pos
10
AA ref
N
AA alt
K
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10088C>A
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
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Powered by MitoWheel

Conservation

PhyloP 100v
-10.594 Conservation Score
PhyloP 470way
-0.323 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.002 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Likely pathogenic Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Medium Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Vus Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
10088C>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
.
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

10088 (C > G)

MT-ND1_5xtc_s_j_VA144I_NB10K MT-ND1_5xtc_s_j_VA144I_NB10K

General info

Mitimpact ID
MI.15026
Chr
chrM
Start
10088
Ref
C
Alt
G
Gene symbol
MT-ND3 Extended gene annotation
Gene position
30
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
AAC/AAG
AA pos
10
AA ref
N
AA alt
K
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10088C>G
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-10.594 Conservation Score
PhyloP 470way
-0.323 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.002 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Likely pathogenic Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Medium Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Vus Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
10088C>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
.
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.
~ 10086 (A/C) 10086 (A/G) 10086 (A/T) 10087 (A/C) 10087 (A/G) 10087 (A/T) 10088 (C/A) 10088 (C/G)
~ 10086 (AAC/CAC) 10086 (AAC/GAC) 10086 (AAC/TAC) 10087 (AAC/ACC) 10087 (AAC/AGC) 10087 (AAC/ATC) 10088 (AAC/AAA) 10088 (AAC/AAG)
MitImpact id MI.15021 MI.15020 MI.15019 MI.15022 MI.15023 MI.15024 MI.15025 MI.15026
Chr chrM chrM chrM chrM chrM chrM chrM chrM
Start 10086 10086 10086 10087 10087 10087 10088 10088
Ref A A A A A A C C
Alt C G T C G T A G
Gene symbol MT-ND3 MT-ND3 MT-ND3 MT-ND3 MT-ND3 MT-ND3 MT-ND3 MT-ND3
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3
Gene position 28 28 28 29 29 29 30 30
Gene start 10059 10059 10059 10059 10059 10059 10059 10059
Gene end 10404 10404 10404 10404 10404 10404 10404 10404
Gene strand + + + + + + + +
Codon substitution AAC/CAC AAC/GAC AAC/TAC AAC/ACC AAC/AGC AAC/ATC AAC/AAA AAC/AAG
AA position 10 10 10 10 10 10 10 10
AA ref N N N N N N N N
AA alt H D Y T S I K K
Functional effect general missense missense missense missense missense missense missense missense
Functional effect detailed missense missense missense missense missense missense missense missense
OMIM id 516002 516002 516002 516002 516002 516002 516002 516002
HGVS NC_012920.1:g.10086A>C NC_012920.1:g.10086A>G NC_012920.1:g.10086A>T NC_012920.1:g.10087A>C NC_012920.1:g.10087A>G NC_012920.1:g.10087A>T NC_012920.1:g.10088C>A NC_012920.1:g.10088C>G
HGNC id 7458 7458 7458 7458 7458 7458 7458 7458
Respiratory Chain complex I I I I I I I I
Ensembl gene id ENSG00000198840 ENSG00000198840 ENSG00000198840 ENSG00000198840 ENSG00000198840 ENSG00000198840 ENSG00000198840 ENSG00000198840
Ensembl transcript id ENST00000361227 ENST00000361227 ENST00000361227 ENST00000361227 ENST00000361227 ENST00000361227 ENST00000361227 ENST00000361227
Ensembl protein id ENSP00000355206 ENSP00000355206 ENSP00000355206 ENSP00000355206 ENSP00000355206 ENSP00000355206 ENSP00000355206 ENSP00000355206
Uniprot id P03897 P03897 P03897 P03897 P03897 P03897 P03897 P03897
Uniprot name NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN
Ncbi gene id 4537 4537 4537 4537 4537 4537 4537 4537
Ncbi protein id YP_003024033.1 YP_003024033.1 YP_003024033.1 YP_003024033.1 YP_003024033.1 YP_003024033.1 YP_003024033.1 YP_003024033.1
PhyloP 100V 1.06 1.06 1.06 2.452 2.452 2.452 -10.594 -10.594
PhyloP 470Way 0.819 0.819 0.819 0.819 0.819 0.819 -0.323 -0.323
PhastCons 100V 0.012 0.012 0.012 0.044 0.044 0.044 0 0
PhastCons 470Way 0.004 0.004 0.004 0.004 0.004 0.004 0.002 0.002
PolyPhen2 probably_damaging possibly_damaging probably_damaging probably_damaging possibly_damaging probably_damaging probably_damaging probably_damaging
PolyPhen2 score 0.98 0.9 0.98 0.94 0.9 0.98 0.94 0.94
SIFT neutral deleterious neutral neutral neutral neutral deleterious deleterious
SIFT score 0.07 0.02 0.15 0.23 0.37 1.0 0.03 0.03
SIFT4G Damaging Tolerated Tolerated Tolerated Tolerated Damaging Damaging Damaging
SIFT4G score 0.035 0.064 0.081 0.456 0.352 0.039 0.019 0.019
VEST Neutral Neutral Neutral Neutral Neutral Neutral Neutral Neutral
VEST pvalue 0.34 0.44 0.14 0.29 0.42 0.16 0.37 0.37
VEST FDR 0.5 0.55 0.4 0.45 0.55 0.45 0.5 0.5
Mitoclass.1 damaging damaging damaging neutral neutral neutral damaging damaging
SNPDryad Pathogenic Pathogenic Pathogenic Pathogenic Neutral Pathogenic Pathogenic Pathogenic
SNPDryad score 0.98 0.94 0.99 0.96 0.81 0.99 1.0 1.0
MutationTaster Polymorphism Polymorphism Polymorphism Polymorphism Polymorphism Polymorphism Polymorphism Polymorphism
MutationTaster score 1 1 1 1 1 1 1 1
MutationTaster converted rankscore 0.08975 0.08975 0.08975 0.08975 0.08975 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae complex_aae complex_aae complex_aae complex_aae complex_aae
MutationTaster AAE N10H N10D N10Y N10T N10S N10I N10K N10K
fathmm Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated
fathmm score 1.98 1.99 1.99 2.04 2.05 2.05 2.02 2.02
fathmm converted rankscore 0.21865 0.21666 0.21666 0.20808 0.20664 0.20664 0.21119 0.21119
AlphaMissense likely_benign likely_benign ambiguous likely_benign likely_benign likely_benign likely_pathogenic likely_pathogenic
AlphaMissense score 0.2959 0.3156 0.3638 0.1562 0.084 0.3169 0.8262 0.8262
CADD Deleterious Neutral Deleterious Neutral Neutral Deleterious Deleterious Deleterious
CADD score 2.839551 2.474545 3.43805 1.313316 1.374813 3.73131 4.088004 3.643217
CADD phred 21.6 19.3 23.0 12.34 12.66 23.3 23.7 23.2
PROVEAN Damaging Damaging Damaging Damaging Damaging Damaging Damaging Damaging
PROVEAN score -3.9 -3.52 -6.14 -4.13 -3.38 -6.66 -4.5 -4.5
MutationAssessor medium medium medium neutral neutral neutral medium medium
MutationAssessor score 2.885 2.19 2.08 0.535 -0.095 0.5 2.535 2.535
EFIN SP Neutral Neutral Neutral Neutral Neutral Neutral Neutral Neutral
EFIN SP score 0.826 0.956 0.842 0.768 0.78 0.818 0.826 0.826
EFIN HD Neutral Neutral Neutral Neutral Neutral Neutral Neutral Neutral
EFIN HD score 0.336 0.572 0.394 0.68 0.636 0.54 0.314 0.314
MLC Neutral Neutral Neutral Neutral Neutral Neutral Neutral Neutral
MLC score 0.48750679 0.48750679 0.48750679 0.47389704 0.47389704 0.47389704 0.45657553 0.45657553
PANTHER score . . . . . . . .
PhD-SNP score . . . . . . . .
APOGEE1 Neutral Pathogenic Neutral Neutral Neutral Neutral Neutral Neutral
APOGEE1 score 0.38 0.56 0.34 0.4 0.37 0.22 0.42 0.42
APOGEE2 VUS- VUS- VUS Likely-benign Likely-benign VUS- VUS VUS
APOGEE2 score 0.369022686911033 0.278915198080987 0.441788970374027 0.227837705260203 0.19198498966252 0.285273950450107 0.426221168429424 0.426221168429424
CAROL deleterious deleterious deleterious neutral neutral deleterious deleterious deleterious
CAROL score 0.99 0.99 0.99 0.95 0.9 0.98 0.99 0.99
Condel neutral neutral neutral neutral neutral deleterious neutral neutral
Condel score 0.05 0.06 0.09 0.15 0.24 0.51 0.05 0.05
COVEC WMV deleterious deleterious deleterious neutral neutral neutral deleterious deleterious
COVEC WMV score 1 4 1 -2 -3 -2 5 5
MtoolBox deleterious deleterious deleterious deleterious deleterious deleterious deleterious deleterious
MtoolBox DS 0.65 0.59 0.68 0.6 0.58 0.67 0.63 0.63
DEOGEN2 Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated
DEOGEN2 score 0.104786 0.096892 0.112459 0.098764 0.088915 0.109427 0.104998 0.104998
DEOGEN2 converted rankscore 0.41467 0.39916 0.42875 0.40290 0.38262 0.42328 0.41507 0.41507
Meta-SNP . . . . . . . .
Meta-SNP score . . . . . . . .
PolyPhen2 transf low impact low impact low impact low impact low impact low impact low impact low impact
PolyPhen2 transf score -2.24 -1.58 -2.24 -1.8 -1.58 -2.24 -1.8 -1.8
SIFT_transf medium impact medium impact medium impact medium impact medium impact high impact medium impact medium impact
SIFT transf score -0.43 -0.75 -0.23 -0.1 0.06 1.85 -0.65 -0.65
MutationAssessor transf medium impact medium impact medium impact medium impact medium impact medium impact medium impact medium impact
MutationAssessor transf score 1.68 1.04 1.04 -0.3 -0.32 -0.06 1.68 1.68
CHASM Neutral Neutral Neutral Neutral Neutral Neutral Neutral Neutral
CHASM pvalue 0.26 0.28 0.33 0.3 0.27 0.24 0.41 0.41
CHASM FDR 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8
ClinVar id . 693260.0 . . . . . .
ClinVar Allele id . 680150.0 . . . . . .
ClinVar CLNDISDB . MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . . . . . .
ClinVar CLNDN . Leigh_syndrome . . . . . .
ClinVar CLNSIG . Benign . . . . . .
MITOMAP Disease Clinical info . Hypertensive end-stage renal disease . . . . . .
MITOMAP Disease Status . Reported . . . . . .
MITOMAP Disease Hom/Het ./. +/- ./. ./. ./. ./. ./. ./.
MITOMAP General GenBank Freq . 0.7606% . . . . . .
MITOMAP General GenBank Seqs . 465 . . . . . .
MITOMAP General Curated refs . 11553319;23563965;10739760;11938495;27217714;16865696;12509511;29987491;17617636;11349229;11532685;16172508;12949126 . . . . . .
MITOMAP Variant Class . polymorphism;disease . . . . . .
gnomAD 3.1 AN . 56433.0 . . . . . .
gnomAD 3.1 AC Homo . 1197.0 . . . . . .
gnomAD 3.1 AF Hom . 0.021211 . . . . . .
gnomAD 3.1 AC Het . 1.0 . . . . . .
gnomAD 3.1 AF Het . 1.77201e-05 . . . . . .
gnomAD 3.1 filter . PASS . . . . . .
HelixMTdb AC Hom . 573.0 . . . . . .
HelixMTdb AF Hom . 0.002923723 . . . . . .
HelixMTdb AC Het . 4.0 . . . . . .
HelixMTdb AF Het . 2.0409934e-05 . . . . . .
HelixMTdb mean ARF . 0.77078 . . . . . .
HelixMTdb max ARF . 0.90909 . . . . . .
ToMMo 54KJPN AC . 2 . . . . . .
ToMMo 54KJPN AF . 3.7e-05 . . . . . .
ToMMo 54KJPN AN . 54302 . . . . . .
COSMIC 90 . . . . . . . .
dbSNP 156 id . rs28358274 . . . . . .
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
For more info, please check the output legend.
0
Details:
0
Score:  
0
  [min -20, max 10]
  • Predicted accelerated evolution:  score <= 0
  • Conserved:  score > 0
Score:  
0
  [min -20, max 12]
  • Predicted accelerated evolution:  score <= 0
  • Conserved:  score > 0
Score:  
0
  [min 0, max 1]
  • Non-conserved:  score <= 0.7
  • Conserved:  score > 0.7 (soft threshold)
Score:  
0
  [min 0, max 1]
  • Non-conserved:  score <= 0.7
  • Conserved:  score > 0.7 (soft threshold)
Score:  
0
  [min 0, max 1]
  • Neutral:  score <= 0.15
  • Possibly damaging:  0.15 < score <= 0.85
  • Probably damaging:  score > 0.85
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.05
  • Deleterious:  score <= 0.05
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.05
  • Deleterious:  score <= 0.05
Score:  
0
  [min -16.13, max 10.64]
  • Neutral:  score > 1.5
  • Deleterious:  score <= 1.5
Score:  
0
  [min 0.0, max 1.0]
  • Likely benign:  score <= 0.34
  • Ambiguous:  0.34 < score < 0.56
  • Likely pathogenic:  score >= 0.56
Score:  
0
  [min -14, max 14]
  • Neutral:  score > -2.5
  • Deleterious:  score <= -2.5 (soft threshold)
Score:  
0
  [min -6, max 6]
  • Neutral:  score <= 0.8
  • Low impact:  0.8 < score <= 1.9
  • Medium impact:  1.9 < score <= 3.5
  • High impact:  score > 3.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.6
  • Damaging:  score <= 0.6
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.28
  • Damaging:  score <= 0.28
Phred score:  
0
  [min 0, max Unlimited]
  • Neutral:  score < 20 (soft threshold)
  • Deleterious:  score >= 20
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5 (soft threshold)
  • Deleterious:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Polymorphism:  score < 0.5
  • Disease causing:  score >= 0.5
P-value:  
0
  [min 0, max 1]
  • Neutral:  p-value > 0.05
  • Pathogenic:  p-value <= 0.05
Score:  
0
  [min 0, max 1]
No hard-thresholds were indicated by authors (ref). Indicatively:
  • Neutral:  score < 0.9
  • Pathogenic:  score >= 0.9
No score. Categorical only
Please refer to Additional File 14: Table S10 for further details.
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.98
  • Deleterious:  score >= 0.98
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Deleterious:  score >= 0.5
Score:  
0
  [min -6, max 6]
  • Neutral:  score < 0
  • Deleterious:  score > 0
  • Inaccurate prediction:  score = 0
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Deleterious:  score >= 0.5
DS score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.43
  • Deleterious:  score >= 0.43
Pathogenicity score:  
0
  [min 0, max 1]
  • Neutral:  score ≤ 0.5
  • Pathogenic:  score > 0.5


Pathogenicity score for this variant:  
0
  [min 0, max 1]
ACMG-AMP curations for mitochondrial variants should use the raw scores. Standalone probabilities are shown below:
  • Benign:  score ≤ 0.062 (prob. ≤ 0.001)
  • Likely-benign:  0.062 < score ≤ 0.265 (0.001 < prob. ≤ 0.1)
  • Low-scoring VUS (VUS-):  0.265 < score ≤ 0.396 (0.1 < prob. ≤ 0.33)
  • VUS:  0.396 < score ≤ 0.544 (0.33 < prob. ≤ 0.66)
  • High-scoring VUS (VUS+):  0.544 < score < 0.716 (0.66 < prob. < 0.9)
  • Likely-pathogenic:  0.716 ≤ score < 0.907 (0.9 ≤ prob. < 0.99)
  • Pathogenic:  score ≥ 0.907 (prob. ≥ 0.99)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1 (soft threshold)
  • Medium impact:  -1 < score < 1.5 (soft threshold)
  • High impact:  score >= 1.5 (soft threshold)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1
  • Medium impact:  -1 < score < 2 (soft threshold)
  • High impact:  score >= 2 (soft threshold)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1
  • Medium impact:  -1 < score < 2 (soft threshold)
  • High impact:  score >= 2 (soft threshold)
P-value:  
0
  [min 0, max 1]
  • Neutral:  FDR > 0.2
  • Driver:  FDR <= 0.2
The frequency of a CPD variant is proportional to the
number of aligned orthologous sequences that
carry a specific human pathogenic variant as
wild-type amino acid on the total number of aligned
sequences.

For more info, please check the output legend