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4219 (G > A)

MT-ND3_5xtc_s_j_VA305I_NB10D

General info

Mitimpact ID
MI.12660
Chr
chrM
Start
4219
Ref
G
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
913
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GTC/ATC
AA pos
305
AA ref
V
AA alt
I
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4219G>A
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.066 Conservation Score
PhyloP 470way
-0.376 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.005 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
Tolerated 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
Benign Score and details of the meta-predictor
CAROL
Neutral 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
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
High impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Low 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
235315
Clinvar ALLELEID
237002
Clinvar CLNDISDB
Medgen:cn517202;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Not provided;

leigh syndrome
Clinvar CLNSIG
Benign/likely benign
MITOMAP Allele
4219G>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0802%
MITOMAP General GenBank Seqs
49
MITOMAP General GenBank Curated refs
20975840 31797714
MITOMAP Variant Class
polymorphism
Gnomad AN
56416
Gnomad AC hom
57
Gnomad AF hom
0.0010103
Gnomad AC het
3
Gnomad AF het
5.31e-05
Gnomad filter
Pass
HelixMTdb AC hom
59
HelixMTdb AF hom
0.000301
HelixMTdb AC het
16
HelixMTdb AF het
8.16e-05
HelixMTdb mean ARF
0.40884
HelixMTdb max ARF
0.97368
ToMMo JPN54K AC
35
ToMMo JPN54K AF
0.000645
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs878853008

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
.

4219 (G > C)

MT-ND3_5xtc_s_j_VA305L_NB10D

General info

Mitimpact ID
MI.12659
Chr
chrM
Start
4219
Ref
G
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
913
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GTC/CTC
AA pos
305
AA ref
V
AA alt
L
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4219G>C
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.066 Conservation Score
PhyloP 470way
-0.376 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.005 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
Tolerated 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
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
High 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
4219G>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56431
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Npg
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
2
HelixMTdb AF het
1.02e-05
HelixMTdb mean ARF
0.23311
HelixMTdb max ARF
0.3375
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
.

4219 (G > T)

MT-ND3_5xtc_s_j_VA305F_NB10D

General info

Mitimpact ID
MI.12658
Chr
chrM
Start
4219
Ref
G
Alt
T
Gene symbol
MT-ND1 Extended gene annotation
Gene position
913
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GTC/TTC
AA pos
305
AA ref
V
AA alt
F
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4219G>T
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.066 Conservation Score
PhyloP 470way
-0.376 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.005 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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
Tolerated 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
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Medium 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
4219G>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
.

4220 (T > A)

MT-ND3_5xtc_s_j_VA305D_NB10D

General info

Mitimpact ID
MI.12661
Chr
chrM
Start
4220
Ref
T
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
914
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GTC/GAC
AA pos
305
AA ref
V
AA alt
D
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4220T>A
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.266 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.005 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Pathogenic Score and details of the predictor
MitoClass 1
Damaging 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 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
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
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Medium 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
4220T>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
.

4220 (T > C)

MT-ND3_5xtc_s_j_VA305A_NB10D

General info

Mitimpact ID
MI.12663
Chr
chrM
Start
4220
Ref
T
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
914
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GTC/GCC
AA pos
305
AA ref
V
AA alt
A
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4220T>C
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.266 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.005 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
Tolerated 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
Benign Score and details of the meta-predictor
CAROL
Neutral 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
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
High impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Low 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
4220T>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
56432
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
2
Gnomad AF het
3.54e-05
Gnomad filter
Pass
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
.

4220 (T > G)

MT-ND3_5xtc_s_j_VA305G_NB10D

General info

Mitimpact ID
MI.12662
Chr
chrM
Start
4220
Ref
T
Alt
G
Gene symbol
MT-ND1 Extended gene annotation
Gene position
914
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GTC/GGC
AA pos
305
AA ref
V
AA alt
G
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4220T>G
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.266 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.005 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Pathogenic 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
Ambiguous Score and details of the predictor
CADD
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Low 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
Neutral 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
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Medium impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Low 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
4220T>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
.
~ 4219 (G/A) 4219 (G/C) 4219 (G/T) 4220 (T/A) 4220 (T/C) 4220 (T/G)
~ 4219 (GTC/ATC) 4219 (GTC/CTC) 4219 (GTC/TTC) 4220 (GTC/GAC) 4220 (GTC/GCC) 4220 (GTC/GGC)
MitImpact id MI.12660 MI.12659 MI.12658 MI.12661 MI.12663 MI.12662
Chr chrM chrM chrM chrM chrM chrM
Start 4219 4219 4219 4220 4220 4220
Ref G G G T T T
Alt A C T A C G
Gene symbol MT-ND1 MT-ND1 MT-ND1 MT-ND1 MT-ND1 MT-ND1
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1
Gene position 913 913 913 914 914 914
Gene start 3307 3307 3307 3307 3307 3307
Gene end 4262 4262 4262 4262 4262 4262
Gene strand + + + + + +
Codon substitution GTC/ATC GTC/CTC GTC/TTC GTC/GAC GTC/GCC GTC/GGC
AA position 305 305 305 305 305 305
AA ref V V V V V V
AA alt I L F D A G
Functional effect general missense missense missense missense missense missense
Functional effect detailed missense missense missense missense missense missense
OMIM id 516000 516000 516000 516000 516000 516000
HGVS NC_012920.1:g.4219G>A NC_012920.1:g.4219G>C NC_012920.1:g.4219G>T NC_012920.1:g.4220T>A NC_012920.1:g.4220T>C NC_012920.1:g.4220T>G
HGNC id 7455 7455 7455 7455 7455 7455
Respiratory Chain complex I I I I I I
Ensembl gene id ENSG00000198888 ENSG00000198888 ENSG00000198888 ENSG00000198888 ENSG00000198888 ENSG00000198888
Ensembl transcript id ENST00000361390 ENST00000361390 ENST00000361390 ENST00000361390 ENST00000361390 ENST00000361390
Ensembl protein id ENSP00000354687 ENSP00000354687 ENSP00000354687 ENSP00000354687 ENSP00000354687 ENSP00000354687
Uniprot id P03886 P03886 P03886 P03886 P03886 P03886
Uniprot name NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN
Ncbi gene id 4535 4535 4535 4535 4535 4535
Ncbi protein id YP_003024026.1 YP_003024026.1 YP_003024026.1 YP_003024026.1 YP_003024026.1 YP_003024026.1
PhyloP 100V 0.066 0.066 0.066 0.266 0.266 0.266
PhyloP 470Way -0.376 -0.376 -0.376 0.458 0.458 0.458
PhastCons 100V 0 0 0 0 0 0
PhastCons 470Way 0.005 0.005 0.005 0.005 0.005 0.005
PolyPhen2 benign benign benign benign benign benign
PolyPhen2 score 0.0 0.0 0.16 0.21 0.0 0.1
SIFT neutral neutral neutral neutral neutral neutral
SIFT score 0.48 1.0 0.43 0.06 0.51 0.16
SIFT4G Tolerated Tolerated Damaging Damaging Tolerated Damaging
SIFT4G score 1.0 0.665 0.011 0.001 0.065 0.001
VEST Neutral Neutral Neutral Pathogenic Neutral Pathogenic
VEST pvalue 0.35 0.22 0.06 0.02 0.16 0.05
VEST FDR 0.5 0.45 0.35 0.35 0.45 0.35
Mitoclass.1 neutral neutral neutral damaging neutral neutral
SNPDryad Neutral Neutral Neutral Neutral Neutral Neutral
SNPDryad score 0.03 0.39 0.65 0.84 0.49 0.86
MutationTaster Polymorphism Polymorphism Polymorphism Polymorphism Polymorphism Polymorphism
MutationTaster score 1.0 1.0 1.0 1.0 1.0 1.0
MutationTaster converted rankscore 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
MutationTaster AAE V305I V305L V305F V305D V305A V305G
fathmm Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated
fathmm score 2.81 2.77 2.7 2.7 2.88 2.7
fathmm converted rankscore 0.10975 0.11407 0.12162 0.12162 0.10291 0.12162
AlphaMissense likely_benign likely_benign likely_benign likely_pathogenic likely_benign ambiguous
AlphaMissense score 0.0781 0.2327 0.2728 0.8355 0.3082 0.4016
CADD Neutral Neutral Neutral Deleterious Neutral Neutral
CADD score -0.859453 -0.553196 1.947693 2.666018 0.563483 2.008732
CADD phred 0.032 0.162 15.88 20.6 7.899 16.27
PROVEAN Tolerated Tolerated Tolerated Damaging Tolerated Damaging
PROVEAN score 0.24 0.01 -1.95 -3.92 -2.01 -4.34
MutationAssessor neutral neutral neutral medium neutral low
MutationAssessor score -1.185 -0.415 0.285 2.25 -0.11 1.555
EFIN SP Neutral Neutral Neutral Neutral Neutral Neutral
EFIN SP score 0.726 0.806 0.764 0.766 0.824 0.726
EFIN HD Neutral Neutral Neutral Neutral Neutral Neutral
EFIN HD score 0.942 0.672 0.626 0.44 0.726 0.456
MLC Neutral Neutral Neutral Neutral Neutral Neutral
MLC score 0.20411612 0.20411612 0.20411612 0.19295069 0.19295069 0.19295069
PANTHER score . . . . . .
PhD-SNP score . . . . . .
APOGEE1 Neutral Neutral Neutral Neutral Neutral Neutral
APOGEE1 score 0.42 0.3 0.36 0.34 0.3 0.38
APOGEE2 Benign Likely-benign Likely-benign VUS Benign VUS-
APOGEE2 score 0.0178600066502164 0.0829289572330553 0.247953448807371 0.474070204093719 0.0614121678783302 0.303199788064632
CAROL neutral neutral neutral neutral neutral neutral
CAROL score 0.52 0.0 0.49 0.93 0.49 0.82
Condel deleterious deleterious deleterious neutral deleterious deleterious
Condel score 0.74 1.0 0.64 0.43 0.76 0.53
COVEC WMV neutral neutral neutral neutral neutral neutral
COVEC WMV score -6 -6 -6 -3 -6 -6
MtoolBox neutral neutral neutral neutral neutral neutral
MtoolBox DS 0.08 0.08 0.16 0.24 0.08 0.15
DEOGEN2 Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated
DEOGEN2 score 0.0078 0.008009 0.04136 0.216519 0.036683 0.10805
DEOGEN2 converted rankscore 0.07183 0.07373 0.25834 0.57870 0.24197 0.42075
Meta-SNP . . . . . .
Meta-SNP score . . . . . .
PolyPhen2 transf high impact high impact medium impact medium impact high impact medium impact
PolyPhen2 transf score 2.07 2.07 -0.08 -0.21 2.07 0.15
SIFT_transf medium impact high impact medium impact medium impact medium impact medium impact
SIFT transf score 0.26 1.96 0.21 -0.4 0.29 -0.13
MutationAssessor transf low impact medium impact medium impact medium impact low impact low impact
MutationAssessor transf score -2.08 -0.86 -0.62 0.74 -1.45 -1.07
CHASM Neutral Neutral Neutral Neutral Neutral Neutral
CHASM pvalue 0.77 0.52 0.36 0.1 0.31 0.24
CHASM FDR 0.85 0.8 0.8 0.8 0.8 0.8
ClinVar id 235315.0 . . . . .
ClinVar Allele id 237002.0 . . . . .
ClinVar CLNDISDB MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . . . . .
ClinVar CLNDN not_provided|Leigh_syndrome . . . . .
ClinVar CLNSIG Benign/Likely_benign . . . . .
MITOMAP Disease Clinical info . . . . . .
MITOMAP Disease Status . . . . . .
MITOMAP Disease Hom/Het ./. ./. ./. ./. ./. ./.
MITOMAP General GenBank Freq 0.0802% 0.0% . . . .
MITOMAP General GenBank Seqs 49 0 . . . .
MITOMAP General Curated refs 20975840;31797714 . . . . .
MITOMAP Variant Class polymorphism polymorphism . . . .
gnomAD 3.1 AN 56416.0 56431.0 . . 56432.0 .
gnomAD 3.1 AC Homo 57.0 0.0 . . 0.0 .
gnomAD 3.1 AF Hom 0.00101035 0.0 . . 0.0 .
gnomAD 3.1 AC Het 3.0 0.0 . . 2.0 .
gnomAD 3.1 AF Het 5.31764e-05 0.0 . . 3.54409e-05 .
gnomAD 3.1 filter PASS npg . . PASS .
HelixMTdb AC Hom 59.0 0.0 . . . .
HelixMTdb AF Hom 0.00030104653 0.0 . . . .
HelixMTdb AC Het 16.0 2.0 . . . .
HelixMTdb AF Het 8.163974e-05 1.0204967e-05 . . . .
HelixMTdb mean ARF 0.40884 0.23311 . . . .
HelixMTdb max ARF 0.97368 0.3375 . . . .
ToMMo 54KJPN AC 35 . . . . .
ToMMo 54KJPN AF 0.000645 . . . . .
ToMMo 54KJPN AN 54302 . . . . .
COSMIC 90 . . . . . .
dbSNP 156 id rs878853008 . . . . .
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