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3736 (G > A)

MT-ND3_5xtc_s_j_VA144I_NB10S MT-ND3_5xtc_s_j_VA144I_NB10H MT-ND3_5xtc_s_j_VA144I_NB10K MT-ND3_5xtc_s_j_VA144I_NB10Y MT-ND3_5xtc_s_j_VA144I_NB10I MT-ND3_5xtc_s_j_VA144I_NB10T MT-ND3_5xtc_s_j_VA144I_NB10D

General info

Mitimpact ID
MI.11645
Chr
chrM
Start
3736
Ref
G
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
430
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GTC/ATC
AA pos
144
AA ref
V
AA alt
I
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3736G>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
7.55 Conservation Score
PhyloP 470way
0.602 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.177 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
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 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
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
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
692393
Clinvar ALLELEID
680929
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
3736G>A
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
Nr/nr
MITOMAP General GenBank Freq
0.1767%
MITOMAP General GenBank Seqs
108
MITOMAP General GenBank Curated refs
11406419 21978175 29987491 16404693 20643099
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56417
Gnomad AC hom
115
Gnomad AF hom
0.0020383
Gnomad AC het
8
Gnomad AF het
0.0001418
Gnomad filter
Pass
HelixMTdb AC hom
149
HelixMTdb AF hom
0.0007602
HelixMTdb AC het
24
HelixMTdb AF het
0.0001224
HelixMTdb mean ARF
0.39152
HelixMTdb max ARF
0.72
ToMMo JPN54K AC
58
ToMMo JPN54K AF
0.001068
ToMMo JPN54K AN
54302
COSMIC 90
COSM6716702
dbSNP 156
rs201513497

Residue interaction

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

Compensated Pathogenic Deviations

Frequency
0.89 CPD variant frequency
AA ref
V
CPD AA alt
I
Aln pos
145
RefSeq protein ID
YP_003856721 , YP_008379047 , NP_008225 , NP_114334 , NP_007835 , YP_006883018
Species name
Lepilemur hubbardorum, Lepilemur ruficaudatus, Pongo pygmaeus, Macaca sylvanus, Pongo abelii, Nomascus gabriellae
Ncbi taxon ID
756882, 78866, 9600, 9546, 9601, 61852

3736 (G > C)

MT-ND3_5xtc_s_j_VA144L_NB10D

General info

Mitimpact ID
MI.11644
Chr
chrM
Start
3736
Ref
G
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
430
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GTC/CTC
AA pos
144
AA ref
V
AA alt
L
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3736G>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
7.55 Conservation Score
PhyloP 470way
0.602 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.177 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
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
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
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
3736G>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
rs201513497

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
.

3736 (G > T)

MT-ND3_5xtc_s_j_VA144F_NB10D

General info

Mitimpact ID
MI.11646
Chr
chrM
Start
3736
Ref
G
Alt
T
Gene symbol
MT-ND1 Extended gene annotation
Gene position
430
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GTC/TTC
AA pos
144
AA ref
V
AA alt
F
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3736G>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
7.55 Conservation Score
PhyloP 470way
0.602 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.177 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
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
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
High 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
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
High 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
3736G>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
.

3737 (T > A)

MT-ND3_5xtc_s_j_VA144D_NB10D

General info

Mitimpact ID
MI.11649
Chr
chrM
Start
3737
Ref
T
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
431
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GTC/GAC
AA pos
144
AA ref
V
AA alt
D
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3737T>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
7.525 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.114 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
Pathogenic 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
High 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-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
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
High 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
3737T>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
.

3737 (T > C)

MT-ND3_5xtc_s_j_VA144A_NB10D

General info

Mitimpact ID
MI.11647
Chr
chrM
Start
3737
Ref
T
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
431
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GTC/GCC
AA pos
144
AA ref
V
AA alt
A
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3737T>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
7.525 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.114 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
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
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
High 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
.
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
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
3737T>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
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.10309
HelixMTdb max ARF
0.10309
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs1603219109

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
.

3737 (T > G)

MT-ND3_5xtc_s_j_VA144G_NB10D

General info

Mitimpact ID
MI.11648
Chr
chrM
Start
3737
Ref
T
Alt
G
Gene symbol
MT-ND1 Extended gene annotation
Gene position
431
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GTC/GGC
AA pos
144
AA ref
V
AA alt
G
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3737T>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
7.525 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.114 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
Pathogenic 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
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
High 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-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
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
High 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
3737T>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
.
~ 3736 (G/A) 3736 (G/C) 3736 (G/T) 3737 (T/A) 3737 (T/C) 3737 (T/G)
~ 3736 (GTC/ATC) 3736 (GTC/CTC) 3736 (GTC/TTC) 3737 (GTC/GAC) 3737 (GTC/GCC) 3737 (GTC/GGC)
MitImpact id MI.11645 MI.11644 MI.11646 MI.11649 MI.11647 MI.11648
Chr chrM chrM chrM chrM chrM chrM
Start 3736 3736 3736 3737 3737 3737
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 430 430 430 431 431 431
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 144 144 144 144 144 144
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.3736G>A NC_012920.1:g.3736G>C NC_012920.1:g.3736G>T NC_012920.1:g.3737T>A NC_012920.1:g.3737T>C NC_012920.1:g.3737T>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 7.55 7.55 7.55 7.525 7.525 7.525
PhyloP 470Way 0.602 0.602 0.602 0.458 0.458 0.458
PhastCons 100V 1 1 1 1 1 1
PhastCons 470Way 0.177 0.177 0.177 0.114 0.114 0.114
PolyPhen2 benign benign benign probably_damaging possibly_damaging probably_damaging
PolyPhen2 score 0.05 0.39 0.11 0.95 0.64 0.93
SIFT neutral neutral neutral neutral neutral neutral
SIFT score 0.47 0.61 0.54 0.16 0.65 0.28
SIFT4G Damaging Damaging Damaging Damaging Damaging Damaging
SIFT4G score 0.029 0.001 0.004 0.0 0.0 0.0
VEST Neutral Neutral Pathogenic Pathogenic Neutral Pathogenic
VEST pvalue 0.41 0.26 0.03 0.01 0.08 0.01
VEST FDR 0.5 0.45 0.35 0.35 0.35 0.35
Mitoclass.1 damaging damaging damaging damaging damaging damaging
SNPDryad Neutral Neutral Pathogenic Pathogenic Neutral Pathogenic
SNPDryad score 0.08 0.69 0.98 0.99 0.87 0.96
MutationTaster Polymorphism Polymorphism Polymorphism Polymorphism Polymorphism Polymorphism
MutationTaster score 0.999605 0.999411 0.999978 0.999944 0.999982 0.999982
MutationTaster converted rankscore 0.20887 0.21230 0.18612 0.19238 0.18198 0.18198
MutationTaster model complex_aae complex_aae complex_aae complex_aae complex_aae complex_aae
MutationTaster AAE V144I V144L V144F V144D V144A V144G
fathmm Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated
fathmm score 2.66 2.45 2.25 2.22 2.27 2.23
fathmm converted rankscore 0.12575 0.15028 0.17761 0.18248 0.17431 0.18083
AlphaMissense likely_benign likely_pathogenic likely_pathogenic likely_pathogenic likely_pathogenic likely_pathogenic
AlphaMissense score 0.1818 0.8802 0.8388 0.9148 0.894 0.7401
CADD Neutral Neutral Neutral Deleterious Neutral Neutral
CADD score 1.679815 1.61597 1.987055 4.207977 1.733053 2.216084
CADD phred 14.29 13.94 16.13 23.9 14.6 17.61
PROVEAN Tolerated Damaging Damaging Damaging Damaging Damaging
PROVEAN score -0.89 -2.71 -4.54 -6.36 -3.64 -6.36
MutationAssessor low medium high high high high
MutationAssessor score 1.7 2.435 4.69 4.69 3.795 4.345
EFIN SP Neutral Neutral Neutral Neutral Neutral Neutral
EFIN SP score 0.684 0.718 0.71 0.728 0.7 0.786
EFIN HD Neutral Neutral Neutral Neutral Neutral Neutral
EFIN HD score 0.604 0.494 0.498 0.492 0.572 0.572
MLC Neutral Neutral Neutral Neutral Neutral Neutral
MLC score 0.34308045 0.34308045 0.34308045 0.33149255 0.33149255 0.33149255
PANTHER score . . . . . .
PhD-SNP score . . . . . .
APOGEE1 Pathogenic Pathogenic Pathogenic Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.7 0.52 0.66 0.71 0.59 0.63
APOGEE2 Likely-benign VUS+ VUS+ Likely-pathogenic VUS Likely-pathogenic
APOGEE2 score 0.202153519417109 0.577378868852128 0.698312049612463 0.813317475589399 0.541663004275382 0.730491888263469
CAROL neutral neutral neutral neutral neutral neutral
CAROL score 0.48 0.35 0.37 0.97 0.57 0.94
Condel deleterious deleterious deleterious neutral deleterious neutral
Condel score 0.71 0.61 0.72 0.11 0.51 0.18
COVEC WMV neutral neutral neutral deleterious . deleterious
COVEC WMV score -6 -3 -2 2 0 2
MtoolBox neutral neutral neutral deleterious deleterious deleterious
MtoolBox DS 0.19 0.34 0.33 0.85 0.54 0.76
DEOGEN2 Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated
DEOGEN2 score 0.031551 0.121584 0.150501 0.369531 0.132945 0.20355
DEOGEN2 converted rankscore 0.22093 0.44465 0.49001 0.73423 0.46334 0.56206
Meta-SNP . . . . . .
Meta-SNP score . . . . . .
PolyPhen2 transf medium impact medium impact medium impact low impact medium impact low impact
PolyPhen2 transf score 0.45 -0.57 0.1 -1.95 -0.99 -1.81
SIFT_transf medium impact medium impact medium impact medium impact medium impact medium impact
SIFT transf score 0.25 0.38 0.31 -0.13 0.43 0.05
MutationAssessor transf medium impact medium impact high impact high impact medium impact high impact
MutationAssessor transf score 0.49 1.1 2.95 2.95 1.52 2.46
CHASM Neutral Neutral Neutral Neutral Neutral Neutral
CHASM pvalue 0.72 0.32 0.28 0.14 0.11 0.31
CHASM FDR 0.85 0.8 0.8 0.8 0.8 0.8
ClinVar id 692393.0 . . . . .
ClinVar Allele id 680929.0 . . . . .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . . . . .
ClinVar CLNDN Leigh_syndrome . . . . .
ClinVar CLNSIG Benign . . . . .
MITOMAP Disease Clinical info LHON . . . . .
MITOMAP Disease Status Reported . . . . .
MITOMAP Disease Hom/Het nr/nr ./. ./. ./. ./. ./.
MITOMAP General GenBank Freq 0.1767% . . . 0.0% .
MITOMAP General GenBank Seqs 108 . . . 0 .
MITOMAP General Curated refs 11406419;21978175;29987491;16404693;20643099 . . . . .
MITOMAP Variant Class polymorphism;disease . . . polymorphism .
gnomAD 3.1 AN 56417.0 . . . 56431.0 .
gnomAD 3.1 AC Homo 115.0 . . . 0.0 .
gnomAD 3.1 AF Hom 0.00203839 . . . 0.0 .
gnomAD 3.1 AC Het 8.0 . . . 0.0 .
gnomAD 3.1 AF Het 0.000141801 . . . 0.0 .
gnomAD 3.1 filter PASS . . . npg .
HelixMTdb AC Hom 149.0 . . . 0.0 .
HelixMTdb AF Hom 0.00076027005 . . . 0.0 .
HelixMTdb AC Het 24.0 . . . 1.0 .
HelixMTdb AF Het 0.0001224596 . . . 5.1024836e-06 .
HelixMTdb mean ARF 0.39152 . . . 0.10309 .
HelixMTdb max ARF 0.72 . . . 0.10309 .
ToMMo 54KJPN AC 58 . . . . .
ToMMo 54KJPN AF 0.001068 . . . . .
ToMMo 54KJPN AN 54302 . . . . .
COSMIC 90 COSM6716702 . . . . .
dbSNP 156 id rs201513497 rs201513497 . . rs1603219109 .
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