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10191 (T > A)

MT-ND1_5xtc_s_j_AA64S_SB45T MT-ND1_5xtc_s_j_AA64V_SB45T

General info

Mitimpact ID
MI.15247
Chr
chrM
Start
10191
Ref
T
Alt
A
Gene symbol
MT-ND3 Extended gene annotation
Gene position
133
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
TCC/ACC
AA pos
45
AA ref
S
AA alt
T
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10191T>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
3.307 Conservation Score
PhyloP 470way
-0.995 Conservation Score
PhastCons 100v
0.998 Conservation Score
PhastCons 470way
0.048 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
Low Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Deleterious 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
10191T>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
56434
Gnomad AC hom
1
Gnomad AF hom
1.77e-05
Gnomad AC het
0
Gnomad AF het
0.0
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
.

10191 (T > C)

MT-ND1_5xtc_s_j_NA126K_SB45P MT-ND1_5xtc_s_j_NA126Y_SB45P MT-ND1_5xtc_s_j_AA64G_SB45P MT-ND1_5xtc_s_j_NA126I_SB45P MT-ND1_5xtc_s_j_AA64T_SB45P MT-ND1_5xtc_s_j_KA62E_SB45P MT-ND1_5xtc_s_j_NA126S_SB45P MT-ND1_5xtc_s_j_NA126T_SB45P MT-ND1_5xtc_s_j_AA64V_SB45P MT-ND1_5xtc_s_j_AA64S_SB45P MT-ND1_5xtc_s_j_KA62T_SB45P MT-ND1_5xtc_s_j_KA62N_SB45P MT-ND1_5xtc_s_j_AA64D_SB45P MT-ND1_5xtc_s_j_NA126H_SB45P MT-ND1_5xtc_s_j_KA62M_SB45P MT-ND1_5xtc_s_j_KA62Q_SB45P MT-ND1_5xtc_s_j_NA126D_SB45P MT-ND1_5xtc_s_j_AA64P_SB45P

General info

Mitimpact ID
MI.15248
Chr
chrM
Start
10191
Ref
T
Alt
C
Gene symbol
MT-ND3 Extended gene annotation
Gene position
133
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
TCC/CCC
AA pos
45
AA ref
S
AA alt
P
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10191T>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
3.307 Conservation Score
PhyloP 470way
-0.995 Conservation Score
PhastCons 100v
0.998 Conservation Score
PhastCons 470way
0.048 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
Disease automatic 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
Medium Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-pathogenic 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
Damaging 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
9712
Clinvar ALLELEID
24751
Clinvar CLNDISDB
Mondo:mondo:0027068, medgen:c4746992, omim:500014;

mondo:mondo:0044970, medgen:c0751651, orphanet:68380;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

mondo:mondo:0100133, medgen:c1838979, orphanet:2609
Clinvar CLNDN
Mitochondrial complex 1 deficiency, mitochondrial type 1;

mitochondrial disease;

leigh syndrome;

mitochondrial complex i deficiency
Clinvar CLNSIG
Pathogenic
MITOMAP Allele
10191T>C
MITOMAP Disease Clinical info
Leigh disease / esoc
MITOMAP Disease Status
Cfrm [p]
MITOMAP Disease Hom/Het
-/+
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
14684687 37038312 28429146 16044424 30461153 19617458 27450679 30128709 37196589 17413873 14705112 17152068 20226758 18402672 18977334 35715829 15972314 23847141 38437941 24642831 26741492 16023078 11456298 21850008 15576045 20064630 17535832 29987491 21364701 30095618 21457906 31261379 20972245
MITOMAP Variant Class
disease
Gnomad AN
56433
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
.
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
rs267606890

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
.

10191 (T > G)

MT-ND1_5xtc_s_j_AA64V_SB45A MT-ND1_5xtc_s_j_AA64S_SB45A

General info

Mitimpact ID
MI.15246
Chr
chrM
Start
10191
Ref
T
Alt
G
Gene symbol
MT-ND3 Extended gene annotation
Gene position
133
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
TCC/GCC
AA pos
45
AA ref
S
AA alt
A
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10191T>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
3.307 Conservation Score
PhyloP 470way
-0.995 Conservation Score
PhastCons 100v
0.998 Conservation Score
PhastCons 470way
0.048 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
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
Deleterious 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
10191T>G
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
56434
Gnomad AC hom
2
Gnomad AF hom
3.54e-05
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
2
HelixMTdb AF hom
1.02e-05
HelixMTdb AC het
0
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
.

10192 (C > A)

MT-ND1_5xtc_s_j_AA64S_SB45Y MT-ND1_5xtc_s_j_AA64V_SB45Y

General info

Mitimpact ID
MI.15250
Chr
chrM
Start
10192
Ref
C
Alt
A
Gene symbol
MT-ND3 Extended gene annotation
Gene position
134
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
TCC/TAC
AA pos
45
AA ref
S
AA alt
Y
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10192C>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
2.698 Conservation Score
PhyloP 470way
-0.992 Conservation Score
PhastCons 100v
0.997 Conservation Score
PhastCons 470way
0.02 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
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
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
Damaging 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
693270
Clinvar ALLELEID
680160
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Likely benign
MITOMAP Allele
10192C>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0065%
MITOMAP General GenBank Seqs
4
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56434
Gnomad AC hom
12
Gnomad AF hom
0.0002126
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
16
HelixMTdb AF hom
8.16e-05
HelixMTdb AC het
0
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
2
ToMMo JPN54K AF
3.7e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs1556423776

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
.

10192 (C > G)

MT-ND1_5xtc_s_j_AA64V_SB45C MT-ND1_5xtc_s_j_AA64S_SB45C

General info

Mitimpact ID
MI.15249
Chr
chrM
Start
10192
Ref
C
Alt
G
Gene symbol
MT-ND3 Extended gene annotation
Gene position
134
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
TCC/TGC
AA pos
45
AA ref
S
AA alt
C
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10192C>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
2.698 Conservation Score
PhyloP 470way
-0.992 Conservation Score
PhastCons 100v
0.997 Conservation Score
PhastCons 470way
0.02 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly 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
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
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
Pathogenic 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
.
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Damaging 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
10192C>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
.

10192 (C > T)

MT-ND1_5xtc_s_j_AA64S_SB45F MT-ND1_5xtc_s_j_AA64V_SB45F

General info

Mitimpact ID
MI.15251
Chr
chrM
Start
10192
Ref
C
Alt
T
Gene symbol
MT-ND3 Extended gene annotation
Gene position
134
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
TCC/TTC
AA pos
45
AA ref
S
AA alt
F
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10192C>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
2.698 Conservation Score
PhyloP 470way
-0.992 Conservation Score
PhastCons 100v
0.997 Conservation Score
PhastCons 470way
0.02 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
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
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
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
Damaging 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
693271
Clinvar ALLELEID
680161
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
10192C>T
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.1734%
MITOMAP General GenBank Seqs
106
MITOMAP General GenBank Curated refs
21978175 21041797 12227465 12802679 28187756 10983718 22561905 16714301
MITOMAP Variant Class
polymorphism
Gnomad AN
56429
Gnomad AC hom
81
Gnomad AF hom
0.0014354
Gnomad AC het
2
Gnomad AF het
3.54e-05
Gnomad filter
Pass
HelixMTdb AC hom
318
HelixMTdb AF hom
0.0016225
HelixMTdb AC het
5
HelixMTdb AF het
2.55e-05
HelixMTdb mean ARF
0.43853
HelixMTdb max ARF
0.88235
ToMMo JPN54K AC
62
ToMMo JPN54K AF
0.001142
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs1556423776

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
.
~ 10191 (T/A) 10191 (T/C) 10191 (T/G) 10192 (C/A) 10192 (C/G) 10192 (C/T)
~ 10191 (TCC/ACC) 10191 (TCC/CCC) 10191 (TCC/GCC) 10192 (TCC/TAC) 10192 (TCC/TGC) 10192 (TCC/TTC)
MitImpact id MI.15247 MI.15248 MI.15246 MI.15250 MI.15249 MI.15251
Chr chrM chrM chrM chrM chrM chrM
Start 10191 10191 10191 10192 10192 10192
Ref T T T C C C
Alt A C G A G T
Gene symbol 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
Gene position 133 133 133 134 134 134
Gene start 10059 10059 10059 10059 10059 10059
Gene end 10404 10404 10404 10404 10404 10404
Gene strand + + + + + +
Codon substitution TCC/ACC TCC/CCC TCC/GCC TCC/TAC TCC/TGC TCC/TTC
AA position 45 45 45 45 45 45
AA ref S S S S S S
AA alt T P A Y C F
Functional effect general missense missense missense missense missense missense
Functional effect detailed missense missense missense missense missense missense
OMIM id 516002 516002 516002 516002 516002 516002
HGVS NC_012920.1:g.10191T>A NC_012920.1:g.10191T>C NC_012920.1:g.10191T>G NC_012920.1:g.10192C>A NC_012920.1:g.10192C>G NC_012920.1:g.10192C>T
HGNC id 7458 7458 7458 7458 7458 7458
Respiratory Chain complex I I I I I I
Ensembl gene id ENSG00000198840 ENSG00000198840 ENSG00000198840 ENSG00000198840 ENSG00000198840 ENSG00000198840
Ensembl transcript id ENST00000361227 ENST00000361227 ENST00000361227 ENST00000361227 ENST00000361227 ENST00000361227
Ensembl protein id ENSP00000355206 ENSP00000355206 ENSP00000355206 ENSP00000355206 ENSP00000355206 ENSP00000355206
Uniprot id P03897 P03897 P03897 P03897 P03897 P03897
Uniprot name NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN
Ncbi gene id 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
PhyloP 100V 3.307 3.307 3.307 2.698 2.698 2.698
PhyloP 470Way -0.995 -0.995 -0.995 -0.992 -0.992 -0.992
PhastCons 100V 0.998 0.998 0.998 0.997 0.997 0.997
PhastCons 470Way 0.048 0.048 0.048 0.02 0.02 0.02
PolyPhen2 benign benign benign benign possibly_damaging benign
PolyPhen2 score 0.09 0.43 0.09 0.0 0.71 0.0
SIFT neutral neutral neutral neutral neutral neutral
SIFT score 0.6 0.3 0.79 0.17 0.08 0.14
SIFT4G Damaging Damaging Damaging Damaging Damaging Damaging
SIFT4G score 0.029 0.001 0.012 0.005 0.0 0.0
VEST Neutral Neutral Neutral Neutral Neutral Neutral
VEST pvalue 0.33 0.12 0.3 0.09 0.11 0.11
VEST FDR 0.5 0.4 0.45 0.35 0.4 0.4
Mitoclass.1 neutral neutral neutral neutral neutral neutral
SNPDryad Neutral Neutral Neutral Neutral Neutral Neutral
SNPDryad score 0.13 0.6 0.1 0.06 0.56 0.54
MutationTaster Polymorphism Disease automatic Polymorphism Polymorphism Polymorphism Polymorphism
MutationTaster score 1 4.91678e-14 1 1 1 1
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 S45T S45P S45A S45Y S45C S45F
fathmm Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated
fathmm score 0.9 0.85 0.91 0.83 0.82 0.84
fathmm converted rankscore 0.45248 0.47130 0.44856 0.47815 0.48142 0.47477
AlphaMissense likely_benign ambiguous likely_benign likely_benign likely_benign ambiguous
AlphaMissense score 0.1187 0.5228 0.1205 0.2785 0.2552 0.3847
CADD Neutral Neutral Neutral Neutral Deleterious Neutral
CADD score 1.815268 2.30741 1.738785 2.196015 3.218955 2.236571
CADD phred 15.08 18.21 14.63 17.48 22.7 17.75
PROVEAN Tolerated Damaging Tolerated Damaging Damaging Damaging
PROVEAN score -1.76 -2.51 -0.84 -3.39 -3.36 -3.55
MutationAssessor low medium low medium medium medium
MutationAssessor score 1.135 2.895 1.575 2.345 2.0 2.09
EFIN SP Damaging Damaging Neutral Neutral Neutral Neutral
EFIN SP score 0.6 0.172 0.764 0.702 0.692 0.62
EFIN HD Neutral Neutral Neutral Neutral Neutral Neutral
EFIN HD score 0.648 0.352 0.814 0.578 0.434 0.542
MLC Deleterious Deleterious Deleterious Neutral Neutral Neutral
MLC score 0.50733297 0.50733297 0.50733297 0.49972841 0.49972841 0.49972841
PANTHER score . . . . . .
PhD-SNP score . . . . . .
APOGEE1 Neutral Pathogenic Neutral Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.4 0.95 0.35 0.53 0.6 0.55
APOGEE2 Likely-benign Likely-pathogenic Likely-benign Likely-benign VUS+ VUS-
APOGEE2 score 0.207107797390288 0.885009891987772 0.123940852115962 0.261702983318272 0.596918866941625 0.315129251318063
CAROL neutral neutral neutral neutral neutral neutral
CAROL score 0.31 0.66 0.11 0.83 0.93 0.86
Condel deleterious neutral deleterious deleterious neutral deleterious
Condel score 0.76 0.44 0.85 0.59 0.19 0.57
COVEC WMV neutral neutral neutral neutral . neutral
COVEC WMV score -3 -3 -3 -3 0 -3
MtoolBox neutral deleterious neutral neutral deleterious neutral
MtoolBox DS 0.16 0.57 0.15 0.19 0.62 0.21
DEOGEN2 Tolerated Damaging Tolerated Damaging Damaging Damaging
DEOGEN2 score 0.369006 0.550626 0.334521 0.559766 0.682177 0.634002
DEOGEN2 converted rankscore 0.73379 0.84778 0.70424 0.85242 0.90678 0.88692
Meta-SNP . . . . . .
Meta-SNP score . . . . . .
PolyPhen2 transf medium impact medium impact medium impact medium impact low impact medium impact
PolyPhen2 transf score 0.19 -0.61 0.19 1.99 -1.07 1.99
SIFT_transf medium impact medium impact medium impact medium impact medium impact medium impact
SIFT transf score 0.29 -0.01 0.51 -0.19 -0.4 -0.25
MutationAssessor transf medium impact medium impact medium impact medium impact medium impact medium impact
MutationAssessor transf score 0.84 1.53 1.07 1.22 1.85 1.28
CHASM Neutral Neutral Neutral Neutral Neutral Neutral
CHASM pvalue 0.48 0.22 0.35 0.2 0.27 0.09
CHASM FDR 0.8 0.8 0.8 0.8 0.8 0.8
ClinVar id . 9712.0 . 693270.0 . 693271.0
ClinVar Allele id . 24751.0 . 680160.0 . 680161.0
ClinVar CLNDISDB . MONDO:MONDO:0027068,MedGen:C4746992,OMIM:500014|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0100133,MedGen:C1838979,Orphanet:2609 . MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506
ClinVar CLNDN . Mitochondrial_complex_1_deficiency,_mitochondrial_type_1|Mitochondrial_disease|Leigh_syndrome|Mitochondrial_complex_I_deficiency . Leigh_syndrome . Leigh_syndrome
ClinVar CLNSIG . Pathogenic . Likely_benign . Benign
MITOMAP Disease Clinical info . Leigh Disease / ESOC . . . .
MITOMAP Disease Status . Cfrm [P] . . . .
MITOMAP Disease Hom/Het ./. -/+ ./. ./. ./. ./.
MITOMAP General GenBank Freq . 0.0% 0.0% 0.0065% . 0.1734%
MITOMAP General GenBank Seqs . 0 0 4 . 106
MITOMAP General Curated refs . 14684687;37038312;28429146;16044424;30461153;19617458;27450679;30128709;37196589;17413873;14705112;17152068;20226758;18402672;18977334;35715829;15972314;23847141;38437941;24642831;26741492;16023078;11456298;21850008;15576045;20064630;17535832;29987491;21364701;30095618;21457906;31261379;20972245 . . . 21978175;21041797;12227465;12802679;28187756;10983718;22561905;16714301
MITOMAP Variant Class . disease polymorphism polymorphism . polymorphism
gnomAD 3.1 AN 56434.0 56433.0 56434.0 56434.0 . 56429.0
gnomAD 3.1 AC Homo 1.0 0.0 2.0 12.0 . 81.0
gnomAD 3.1 AF Hom 1.77198e-05 0.0 3.54396e-05 0.000212638 . 0.00143543
gnomAD 3.1 AC Het 0.0 0.0 0.0 0.0 . 2.0
gnomAD 3.1 AF Het 0.0 0.0 0.0 0.0 . 3.54428e-05
gnomAD 3.1 filter PASS npg PASS PASS . PASS
HelixMTdb AC Hom . . 2.0 16.0 . 318.0
HelixMTdb AF Hom . . 1.0204967e-05 8.163974e-05 . 0.0016225898
HelixMTdb AC Het . . 0.0 0.0 . 5.0
HelixMTdb AF Het . . 0.0 0.0 . 2.5512418e-05
HelixMTdb mean ARF . . . . . 0.43853
HelixMTdb max ARF . . . . . 0.88235
ToMMo 54KJPN AC . . . 2 . 62
ToMMo 54KJPN AF . . . 3.7e-05 . 0.001142
ToMMo 54KJPN AN . . . 54302 . 54302
COSMIC 90 . . . . . .
dbSNP 156 id . rs267606890 . rs1556423776 . rs1556423776
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