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10680 (G > A)

MT-ND6_5xtc_m_k_TA71M_AB71T MT-ND6_5xtc_m_k_TA71A_AB71T MT-ND6_5xtc_m_k_TA71K_AB71T MT-ND6_5xtc_m_k_TA71P_AB71T

General info

Mitimpact ID
MI.16139
Chr
chrM
Start
10680
Ref
G
Alt
A
Gene symbol
MT-ND4L Extended gene annotation
Gene position
211
Gene start
10470
Gene end
10766
Gene strand
+
Codon substitution
GCA/ACA
AA pos
71
AA ref
A
AA alt
T
Functional effect
missense
OMIM ID
516004
HGVS
NC_012920.1:g.10680G>A
HGNC ID
7460
RC complex
I
Ensembl gene ID
ENSG00000212907
Ensembl protein ID
ENSP00000354728
Ensembl transcript ID
ENST00000361335
Uniprot ID
P03901
Uniprot name
NU4LM_HUMAN
Ncbi gene ID
4539
Ncbi protein ID
YP_003024034.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
4.764 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.495 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
Disease 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
.
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
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
693310
Clinvar ALLELEID
680200
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Likely benign
MITOMAP Allele
10680G>A
MITOMAP Disease Clinical info
Lhon / synergistic combo 10680a + 12033g + 14258a
MITOMAP Disease Status
Reported / possibly synergistic
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.0294%
MITOMAP General GenBank Seqs
18
MITOMAP General GenBank Curated refs
29444077 29987491 24448545 19394449 22400981 20643099
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56423
Gnomad AC hom
12
Gnomad AF hom
0.0002126
Gnomad AC het
8
Gnomad AF het
0.0001417
Gnomad filter
Pass
HelixMTdb AC hom
45
HelixMTdb AF hom
0.0002296
HelixMTdb AC het
14
HelixMTdb AF het
7.14e-05
HelixMTdb mean ARF
0.37275
HelixMTdb max ARF
0.86538
ToMMo JPN54K AC
5
ToMMo JPN54K AF
9.2e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs1603222945

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
.

10680 (G > C)

General info

Mitimpact ID
MI.16141
Chr
chrM
Start
10680
Ref
G
Alt
C
Gene symbol
MT-ND4L Extended gene annotation
Gene position
211
Gene start
10470
Gene end
10766
Gene strand
+
Codon substitution
GCA/CCA
AA pos
71
AA ref
A
AA alt
P
Functional effect
missense
OMIM ID
516004
HGVS
NC_012920.1:g.10680G>C
HGNC ID
7460
RC complex
I
Ensembl gene ID
ENSG00000212907
Ensembl protein ID
ENSP00000354728
Ensembl transcript ID
ENST00000361335
Uniprot ID
P03901
Uniprot name
NU4LM_HUMAN
Ncbi gene ID
4539
Ncbi protein ID
YP_003024034.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
4.764 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.495 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor
MutationTaster
Disease 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
.
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
Vus+ Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
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
10680G>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
.
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

Residue interaction

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

Compensated Pathogenic Deviations

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

10680 (G > T)

General info

Mitimpact ID
MI.16140
Chr
chrM
Start
10680
Ref
G
Alt
T
Gene symbol
MT-ND4L Extended gene annotation
Gene position
211
Gene start
10470
Gene end
10766
Gene strand
+
Codon substitution
GCA/TCA
AA pos
71
AA ref
A
AA alt
S
Functional effect
missense
OMIM ID
516004
HGVS
NC_012920.1:g.10680G>T
HGNC ID
7460
RC complex
I
Ensembl gene ID
ENSG00000212907
Ensembl protein ID
ENSP00000354728
Ensembl transcript ID
ENST00000361335
Uniprot ID
P03901
Uniprot name
NU4LM_HUMAN
Ncbi gene ID
4539
Ncbi protein ID
YP_003024034.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
4.764 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.495 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
Disease 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
.
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
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
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

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

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
10680G>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
.

10681 (C > A)

General info

Mitimpact ID
MI.16144
Chr
chrM
Start
10681
Ref
C
Alt
A
Gene symbol
MT-ND4L Extended gene annotation
Gene position
212
Gene start
10470
Gene end
10766
Gene strand
+
Codon substitution
GCA/GAA
AA pos
71
AA ref
A
AA alt
E
Functional effect
missense
OMIM ID
516004
HGVS
NC_012920.1:g.10681C>A
HGNC ID
7460
RC complex
I
Ensembl gene ID
ENSG00000212907
Ensembl protein ID
ENSP00000354728
Ensembl transcript ID
ENST00000361335
Uniprot ID
P03901
Uniprot name
NU4LM_HUMAN
Ncbi gene ID
4539
Ncbi protein ID
YP_003024034.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
3.193 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0.994 Conservation Score
PhastCons 470way
0.46 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
Disease 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
.
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
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
10681C>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
.

10681 (C > G)

General info

Mitimpact ID
MI.16143
Chr
chrM
Start
10681
Ref
C
Alt
G
Gene symbol
MT-ND4L Extended gene annotation
Gene position
212
Gene start
10470
Gene end
10766
Gene strand
+
Codon substitution
GCA/GGA
AA pos
71
AA ref
A
AA alt
G
Functional effect
missense
OMIM ID
516004
HGVS
NC_012920.1:g.10681C>G
HGNC ID
7460
RC complex
I
Ensembl gene ID
ENSG00000212907
Ensembl protein ID
ENSP00000354728
Ensembl transcript ID
ENST00000361335
Uniprot ID
P03901
Uniprot name
NU4LM_HUMAN
Ncbi gene ID
4539
Ncbi protein ID
YP_003024034.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
3.193 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0.994 Conservation Score
PhastCons 470way
0.46 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 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
.
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
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
10681C>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
.

10681 (C > T)

General info

Mitimpact ID
MI.16142
Chr
chrM
Start
10681
Ref
C
Alt
T
Gene symbol
MT-ND4L Extended gene annotation
Gene position
212
Gene start
10470
Gene end
10766
Gene strand
+
Codon substitution
GCA/GTA
AA pos
71
AA ref
A
AA alt
V
Functional effect
missense
OMIM ID
516004
HGVS
NC_012920.1:g.10681C>T
HGNC ID
7460
RC complex
I
Ensembl gene ID
ENSG00000212907
Ensembl protein ID
ENSP00000354728
Ensembl transcript ID
ENST00000361335
Uniprot ID
P03901
Uniprot name
NU4LM_HUMAN
Ncbi gene ID
4539
Ncbi protein ID
YP_003024034.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
3.193 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0.994 Conservation Score
PhastCons 470way
0.46 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
Disease 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
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
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
10681C>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
.
~ 10680 (G/A) 10680 (G/C) 10680 (G/T) 10681 (C/A) 10681 (C/G) 10681 (C/T)
~ 10680 (GCA/ACA) 10680 (GCA/CCA) 10680 (GCA/TCA) 10681 (GCA/GAA) 10681 (GCA/GGA) 10681 (GCA/GTA)
MitImpact id MI.16139 MI.16141 MI.16140 MI.16144 MI.16143 MI.16142
Chr chrM chrM chrM chrM chrM chrM
Start 10680 10680 10680 10681 10681 10681
Ref G G G C C C
Alt A C T A G T
Gene symbol MT-ND4L MT-ND4L MT-ND4L MT-ND4L MT-ND4L MT-ND4L
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4L mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4L mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4L mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4L mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4L mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4L
Gene position 211 211 211 212 212 212
Gene start 10470 10470 10470 10470 10470 10470
Gene end 10766 10766 10766 10766 10766 10766
Gene strand + + + + + +
Codon substitution GCA/ACA GCA/CCA GCA/TCA GCA/GAA GCA/GGA GCA/GTA
AA position 71 71 71 71 71 71
AA ref A A A A A A
AA alt T P S E G V
Functional effect general missense missense missense missense missense missense
Functional effect detailed missense missense missense missense missense missense
OMIM id 516004 516004 516004 516004 516004 516004
HGVS NC_012920.1:g.10680G>A NC_012920.1:g.10680G>C NC_012920.1:g.10680G>T NC_012920.1:g.10681C>A NC_012920.1:g.10681C>G NC_012920.1:g.10681C>T
HGNC id 7460 7460 7460 7460 7460 7460
Respiratory Chain complex I I I I I I
Ensembl gene id ENSG00000212907 ENSG00000212907 ENSG00000212907 ENSG00000212907 ENSG00000212907 ENSG00000212907
Ensembl transcript id ENST00000361335 ENST00000361335 ENST00000361335 ENST00000361335 ENST00000361335 ENST00000361335
Ensembl protein id ENSP00000354728 ENSP00000354728 ENSP00000354728 ENSP00000354728 ENSP00000354728 ENSP00000354728
Uniprot id P03901 P03901 P03901 P03901 P03901 P03901
Uniprot name NU4LM_HUMAN NU4LM_HUMAN NU4LM_HUMAN NU4LM_HUMAN NU4LM_HUMAN NU4LM_HUMAN
Ncbi gene id 4539 4539 4539 4539 4539 4539
Ncbi protein id YP_003024034.1 YP_003024034.1 YP_003024034.1 YP_003024034.1 YP_003024034.1 YP_003024034.1
PhyloP 100V 4.764 4.764 4.764 3.193 3.193 3.193
PhyloP 470Way 0.848 0.848 0.848 0.65 0.65 0.65
PhastCons 100V 1 1 1 0.994 0.994 0.994
PhastCons 470Way 0.495 0.495 0.495 0.46 0.46 0.46
PolyPhen2 benign probably_damaging possibly_damaging possibly_damaging benign possibly_damaging
PolyPhen2 score 0.05 0.95 0.64 0.87 0.08 0.75
SIFT neutral neutral neutral neutral neutral neutral
SIFT score 0.09 0.07 0.25 0.26 0.51 0.27
SIFT4G Damaging Damaging Damaging Damaging Damaging Damaging
SIFT4G score 0.024 0.001 0.001 0.006 0.023 0.0
VEST Neutral Neutral Neutral Neutral Neutral Neutral
VEST pvalue 0.38 0.23 0.48 0.17 0.4 0.44
VEST FDR 0.5 0.45 0.55 0.45 0.5 0.55
Mitoclass.1 damaging damaging neutral damaging neutral damaging
SNPDryad Neutral Neutral Neutral Neutral Neutral Neutral
SNPDryad score 0.02 0.86 0.63 0.84 0.63 0.58
MutationTaster Disease Disease Disease Disease Disease Disease
MutationTaster score 0.972727 0.992048 0.93919 0.999885 0.999739 0.999791
MutationTaster converted rankscore 0.38968 0.4154 0.37252 0.50402 0.48635 0.49177
MutationTaster model simple_aae simple_aae simple_aae simple_aae simple_aae simple_aae
MutationTaster AAE A71T A71P A71S A71E A71G A71V
fathmm Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated
fathmm score 1.94 1.67 1.76 1.7 1.72 1.77
fathmm converted rankscore 0.22678 0.27331 0.25996 0.26885 0.26588 0.25841
AlphaMissense ambiguous likely_pathogenic likely_benign likely_pathogenic ambiguous likely_pathogenic
AlphaMissense score 0.3407 0.8668 0.3369 0.8405 0.3519 0.6913
CADD Neutral Deleterious Neutral Deleterious Neutral Deleterious
CADD score 2.352841 3.83081 2.173034 4.398102 2.038522 4.115813
CADD phred 18.51 23.4 17.33 24.1 16.46 23.8
PROVEAN Damaging Damaging Tolerated Damaging Damaging Damaging
PROVEAN score -2.98 -4.46 -2.47 -4.46 -3.44 -3.53
MutationAssessor . . . . . high
MutationAssessor score . . . . . 5.015
EFIN SP Neutral Damaging Neutral Neutral Neutral Neutral
EFIN SP score 0.724 0.564 0.652 0.614 0.674 0.648
EFIN HD Neutral Neutral Neutral Neutral Neutral Neutral
EFIN HD score 0.596 0.288 0.388 0.356 0.464 0.292
MLC Deleterious Deleterious Deleterious Deleterious Deleterious Deleterious
MLC score 0.94012916 0.94012916 0.94012916 0.94148711 0.94148711 0.94148711
PANTHER score . . . . . .
PhD-SNP score . . . . . .
APOGEE1 Neutral Pathogenic Neutral Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.42 0.56 0.42 0.7 0.55 0.69
APOGEE2 VUS- VUS+ VUS+ Likely-pathogenic VUS Likely-pathogenic
APOGEE2 score 0.366809803095136 0.696166817262209 0.595831997453415 0.805148351382631 0.526567874747992 0.813041169444244
CAROL neutral deleterious neutral neutral neutral neutral
CAROL score 0.9 0.99 0.77 0.9 0.42 0.82
Condel deleterious neutral neutral neutral deleterious neutral
Condel score 0.52 0.06 0.31 0.2 0.72 0.26
COVEC WMV neutral deleterious . deleterious neutral deleterious
COVEC WMV score -2 2 0 1 -6 1
MtoolBox neutral deleterious deleterious deleterious neutral deleterious
MtoolBox DS 0.31 0.86 0.68 0.82 0.23 0.7
DEOGEN2 Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated
DEOGEN2 score 0.177563 0.402659 0.177072 0.402659 0.173134 0.176738
DEOGEN2 converted rankscore 0.52791 0.75962 0.52724 0.75962 0.52190 0.52678
Meta-SNP . . . . . .
Meta-SNP score . . . . . .
PolyPhen2 transf medium impact low impact low impact low impact medium impact low impact
PolyPhen2 transf score 0.37 -1.97 -1.03 -1.56 0.17 -1.24
SIFT_transf medium impact medium impact medium impact medium impact medium impact medium impact
SIFT transf score -0.35 -0.41 -0.06 -0.04 0.22 -0.03
MutationAssessor transf high impact high impact medium impact high impact medium impact high impact
MutationAssessor transf score 2.21 2.67 1.31 2.67 0.4 2.38
CHASM Neutral Neutral Neutral Neutral Neutral Neutral
CHASM pvalue 0.7 0.58 0.64 0.51 0.73 0.69
CHASM FDR 0.85 0.8 0.8 0.8 0.85 0.85
ClinVar id 693310.0 . . . . .
ClinVar Allele id 680200.0 . . . . .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . . . . .
ClinVar CLNDN Leigh_syndrome . . . . .
ClinVar CLNSIG Likely_benign . . . . .
MITOMAP Disease Clinical info LHON / synergistic combo 10680A + 12033G + 14258A . . . . .
MITOMAP Disease Status Reported / possibly synergistic . . . . .
MITOMAP Disease Hom/Het +/- ./. ./. ./. ./. ./.
MITOMAP General GenBank Freq 0.0294% . . . . .
MITOMAP General GenBank Seqs 18 . . . . .
MITOMAP General Curated refs 29444077;29987491;24448545;19394449;22400981;20643099 . . . . .
MITOMAP Variant Class polymorphism;disease . . . . .
gnomAD 3.1 AN 56423.0 . . . . .
gnomAD 3.1 AC Homo 12.0 . . . . .
gnomAD 3.1 AF Hom 0.000212679 . . . . .
gnomAD 3.1 AC Het 8.0 . . . . .
gnomAD 3.1 AF Het 0.000141786 . . . . .
gnomAD 3.1 filter PASS . . . . .
HelixMTdb AC Hom 45.0 . . . . .
HelixMTdb AF Hom 0.00022961175 . . . . .
HelixMTdb AC Het 14.0 . . . . .
HelixMTdb AF Het 7.143477e-05 . . . . .
HelixMTdb mean ARF 0.37275 . . . . .
HelixMTdb max ARF 0.86538 . . . . .
ToMMo 54KJPN AC 5 . . . . .
ToMMo 54KJPN AF 9.2e-05 . . . . .
ToMMo 54KJPN AN 54302 . . . . .
COSMIC 90 . . . . . .
dbSNP 156 id rs1603222945 . . . . .
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