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3490 (A > C)

MT-ND3_5xtc_s_j_KA62Q_SB45P

General info

Mitimpact ID
MI.11142
Chr
chrM
Start
3490
Ref
A
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
184
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
AAA/CAA
AA pos
62
AA ref
K
AA alt
Q
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3490A>C
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.474 Conservation Score
PhyloP 470way
-0.91 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.012 Conservation Score

Pathogenicity predictors

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

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
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
3490A>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
.

3490 (A > G)

MT-ND3_5xtc_s_j_KA62E_SB45P

General info

Mitimpact ID
MI.11141
Chr
chrM
Start
3490
Ref
A
Alt
G
Gene symbol
MT-ND1 Extended gene annotation
Gene position
184
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
AAA/GAA
AA pos
62
AA ref
K
AA alt
E
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3490A>G
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.474 Conservation Score
PhyloP 470way
-0.91 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.012 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
Deleterious Score and details of the predictor
PROVEAN
Tolerated Score and details of the predictor
Mutation Assessor
Medium Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
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
High impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
3490A>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
.

3491 (A > C)

MT-ND3_5xtc_s_j_KA62T_SB45P

General info

Mitimpact ID
MI.11143
Chr
chrM
Start
3491
Ref
A
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
185
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
AAA/ACA
AA pos
62
AA ref
K
AA alt
T
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3491A>C
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.374 Conservation Score
PhyloP 470way
-0.292 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.015 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
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Low Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
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
3491A>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
.

3491 (A > T)

MT-ND3_5xtc_s_j_KA62M_SB45P

General info

Mitimpact ID
MI.11144
Chr
chrM
Start
3491
Ref
A
Alt
T
Gene symbol
MT-ND1 Extended gene annotation
Gene position
185
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
AAA/ATA
AA pos
62
AA ref
K
AA alt
M
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3491A>T
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.374 Conservation Score
PhyloP 470way
-0.292 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.015 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
.
fathmm
.
AlphaMissense
Ambiguous Score and details of the predictor
CADD
Deleterious 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
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Vus- Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
.
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
3491A>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
.

3492 (A > C)

MT-ND3_5xtc_s_j_KA62N_SB45P MT-ND3_5xtc_s_j_KA62N_SB45P

General info

Mitimpact ID
MI.11146
Chr
chrM
Start
3492
Ref
A
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
186
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
AAA/AAC
AA pos
62
AA ref
K
AA alt
N
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3492A>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
-5.732 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.024 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 pathogenic Score and details of the predictor
CADD
Deleterious 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
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
692358
Clinvar ALLELEID
680894
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Likely benign
MITOMAP Allele
3492A>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56222
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
rs878950749

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
.

3492 (A > T)

MT-ND3_5xtc_s_j_KA62N_SB45P MT-ND3_5xtc_s_j_KA62N_SB45P

General info

Mitimpact ID
MI.11145
Chr
chrM
Start
3492
Ref
A
Alt
T
Gene symbol
MT-ND1 Extended gene annotation
Gene position
186
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
AAA/AAT
AA pos
62
AA ref
K
AA alt
N
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3492A>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
-5.732 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.024 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 pathogenic Score and details of the predictor
CADD
Deleterious 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
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
3492A>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
.
~ 3490 (A/C) 3490 (A/G) 3491 (A/C) 3491 (A/T) 3492 (A/C) 3492 (A/T)
~ 3490 (AAA/CAA) 3490 (AAA/GAA) 3491 (AAA/ACA) 3491 (AAA/ATA) 3492 (AAA/AAC) 3492 (AAA/AAT)
MitImpact id MI.11142 MI.11141 MI.11143 MI.11144 MI.11146 MI.11145
Chr chrM chrM chrM chrM chrM chrM
Start 3490 3490 3491 3491 3492 3492
Ref A A A A A A
Alt C G C T C T
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 184 184 185 185 186 186
Gene start 3307 3307 3307 3307 3307 3307
Gene end 4262 4262 4262 4262 4262 4262
Gene strand + + + + + +
Codon substitution AAA/CAA AAA/GAA AAA/ACA AAA/ATA AAA/AAC AAA/AAT
AA position 62 62 62 62 62 62
AA ref K K K K K K
AA alt Q E T M N N
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.3490A>C NC_012920.1:g.3490A>G NC_012920.1:g.3491A>C NC_012920.1:g.3491A>T NC_012920.1:g.3492A>C NC_012920.1:g.3492A>T
HGNC id 7455 7455 7455 7455 7455 7455
Respiratory Chain complex I I I I I I
Ensembl gene id ENSG00000198888 ENSG00000198888 ENSG00000198888 ENSG00000198888 ENSG00000198888 ENSG00000198888
Ensembl transcript id ENST00000361390 ENST00000361390 ENST00000361390 ENST00000361390 ENST00000361390 ENST00000361390
Ensembl protein id ENSP00000354687 ENSP00000354687 ENSP00000354687 ENSP00000354687 ENSP00000354687 ENSP00000354687
Uniprot id P03886 P03886 P03886 P03886 P03886 P03886
Uniprot name NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN
Ncbi gene id 4535 4535 4535 4535 4535 4535
Ncbi protein id YP_003024026.1 YP_003024026.1 YP_003024026.1 YP_003024026.1 YP_003024026.1 YP_003024026.1
PhyloP 100V 0.474 0.474 0.374 0.374 -5.732 -5.732
PhyloP 470Way -0.91 -0.91 -0.292 -0.292 0.58 0.58
PhastCons 100V 0 0 0 0 0 0
PhastCons 470Way 0.012 0.012 0.015 0.015 0.024 0.024
PolyPhen2 benign benign benign possibly_damaging benign benign
PolyPhen2 score 0.02 0.18 0.41 0.58 0.26 0.26
SIFT neutral neutral neutral neutral neutral neutral
SIFT score 0.59 1.0 0.59 0.12 0.51 0.51
SIFT4G Tolerated Damaging Damaging Damaging Damaging Damaging
SIFT4G score 0.11 0.009 0.001 0.0 0.001 0.001
VEST Neutral Neutral Neutral Neutral Neutral Neutral
VEST pvalue 0.39 0.26 0.14 0.12 0.5 0.5
VEST FDR 0.5 0.45 0.4 0.4 0.6 0.6
Mitoclass.1 neutral neutral neutral neutral neutral neutral
SNPDryad Neutral Neutral Neutral Neutral Neutral Neutral
SNPDryad score 0.59 0.74 0.75 0.78 0.59 0.59
MutationTaster Polymorphism Polymorphism Polymorphism . Polymorphism Polymorphism
MutationTaster score 0.999995 0.999997 1 . 1 1
MutationTaster converted rankscore 0.08975 0.08975 0.08975 . 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae . complex_aae complex_aae
MutationTaster AAE K62Q K62E K62T . K62N K62N
fathmm Tolerated Tolerated Tolerated . Tolerated Tolerated
fathmm score 2.76 2.77 2.81 . 2.75 2.75
fathmm converted rankscore 0.11515 0.11407 0.10975 . 0.11622 0.11622
AlphaMissense likely_benign ambiguous ambiguous ambiguous likely_pathogenic likely_pathogenic
AlphaMissense score 0.198 0.4773 0.3827 0.3462 0.7258 0.7258
CADD Neutral Deleterious Deleterious Deleterious Deleterious Deleterious
CADD score 2.197908 3.924795 3.512185 3.744075 3.746406 3.819756
CADD phred 17.49 23.5 23.1 23.3 23.3 23.4
PROVEAN Tolerated Tolerated Damaging Tolerated Tolerated Tolerated
PROVEAN score -0.29 -1.36 -2.51 -2.33 -1.59 -1.59
MutationAssessor low medium low . low low
MutationAssessor score 1.555 2.32 0.935 . 1.63 1.63
EFIN SP Neutral Neutral Neutral Neutral Neutral Neutral
EFIN SP score 0.82 0.844 0.692 0.708 0.68 0.68
EFIN HD Neutral Neutral Neutral Neutral Neutral Neutral
EFIN HD score 0.966 0.698 0.658 0.606 0.67 0.67
MLC Neutral Neutral Neutral Neutral Neutral Neutral
MLC score 0.3458869 0.3458869 0.33321263 0.33321263 0.32428028 0.32428028
PANTHER score . . . . . .
PhD-SNP score . . . . . .
APOGEE1 Neutral Neutral Neutral Neutral Neutral Neutral
APOGEE1 score 0.36 0.25 0.3 0.41 0.38 0.38
APOGEE2 Likely-benign Likely-benign Likely-benign VUS- Likely-benign Likely-benign
APOGEE2 score 0.153817425150168 0.120080038285879 0.250683507845739 0.284336980000649 0.185893546384039 0.185893546384039
CAROL neutral neutral neutral neutral neutral neutral
CAROL score 0.38 0.18 0.37 0.88 0.39 0.39
Condel deleterious deleterious deleterious neutral deleterious deleterious
Condel score 0.79 0.91 0.59 0.27 0.63 0.63
COVEC WMV neutral neutral neutral neutral neutral neutral
COVEC WMV score -6 -3 -6 -3 -6 -6
MtoolBox neutral neutral neutral deleterious neutral neutral
MtoolBox DS 0.16 0.27 0.37 0.5 0.38 0.38
DEOGEN2 Tolerated Tolerated Tolerated . Tolerated Tolerated
DEOGEN2 score 0.009596 0.02465 0.068829 . 0.023898 0.023898
DEOGEN2 converted rankscore 0.08729 0.18583 0.33555 . 0.18158 0.18158
Meta-SNP . . . . . .
Meta-SNP score . . . . . .
PolyPhen2 transf medium impact medium impact medium impact medium impact medium impact medium impact
PolyPhen2 transf score 0.84 -0.13 -0.6 -0.88 -0.32 -0.32
SIFT_transf medium impact high impact medium impact medium impact medium impact medium impact
SIFT transf score 0.36 1.96 0.36 -0.21 0.29 0.29
MutationAssessor transf medium impact medium impact medium impact medium impact medium impact medium impact
MutationAssessor transf score -0.04 0.52 -0.71 -0.27 -0.06 -0.06
CHASM Neutral Neutral Neutral Neutral Neutral Neutral
CHASM pvalue 0.36 0.42 0.2 0.19 0.34 0.34
CHASM FDR 0.8 0.8 0.8 0.8 0.8 0.8
ClinVar id . . . . 692358.0 .
ClinVar Allele id . . . . 680894.0 .
ClinVar CLNDISDB . . . . MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 .
ClinVar CLNDN . . . . Leigh_syndrome .
ClinVar CLNSIG . . . . Likely_benign .
MITOMAP Disease Clinical info . . . . . .
MITOMAP Disease Status . . . . . .
MITOMAP Disease Hom/Het ./. ./. ./. ./. ./. ./.
MITOMAP General GenBank Freq . . . . 0.0016% .
MITOMAP General GenBank Seqs . . . . 1 .
MITOMAP General Curated refs . . . . . .
MITOMAP Variant Class . . . . polymorphism .
gnomAD 3.1 AN . . . . 56222.0 .
gnomAD 3.1 AC Homo . . . . 0.0 .
gnomAD 3.1 AF Hom . . . . 0.0 .
gnomAD 3.1 AC Het . . . . 0.0 .
gnomAD 3.1 AF Het . . . . 0.0 .
gnomAD 3.1 filter . . . . npg .
HelixMTdb AC Hom . . . . . .
HelixMTdb AF Hom . . . . . .
HelixMTdb AC Het . . . . . .
HelixMTdb AF Het . . . . . .
HelixMTdb mean ARF . . . . . .
HelixMTdb max ARF . . . . . .
ToMMo 54KJPN AC . . . . . .
ToMMo 54KJPN AF . . . . . .
ToMMo 54KJPN AN . . . . . .
COSMIC 90 . . . . . .
dbSNP 156 id . . . . rs878950749 .
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