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14482 (C > A)

General info

Mitimpact ID
MI.23786
Chr
chrM
Start
14482
Ref
C
Alt
A
Gene symbol
MT-ND6 Extended gene annotation
Gene position
192
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
ATG/ATT
AA pos
64
AA ref
M
AA alt
I
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14482C>A
HGNC ID
7462
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot ID
P03923
Uniprot name
NU6M_HUMAN
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
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Conservation

PhyloP 100v
-3.832 Conservation Score
PhyloP 470way
-0.165 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.958 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
Tolerated Score and details of the predictor
Mutation Assessor
Medium Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
Neutral Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Pathogenic 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
Disease Score and details of the meta-predictor

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
9693
Clinvar ALLELEID
24732
Clinvar CLNDISDB
Mondo:mondo:0044970, medgen:c0751651, orphanet:68380;

human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:104
Clinvar CLNDN
Mitochondrial disease;

leber optic atrophy
Clinvar CLNSIG
Likely pathogenic
MITOMAP Allele
14482C>A
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Cfrm [lp]
MITOMAP Disease Hom/Het
+/+
MITOMAP General GenBank Freq
0.0033%
MITOMAP General GenBank Seqs
2
MITOMAP General GenBank Curated refs
12112086 22879922 12150954 18402672 15972314 19319978 29987491 20301353 16532388 11931086 17122117 21457906 29253894
MITOMAP Variant Class
disease
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
rs199476108

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
.

14482 (C > G)

General info

Mitimpact ID
MI.23787
Chr
chrM
Start
14482
Ref
C
Alt
G
Gene symbol
MT-ND6 Extended gene annotation
Gene position
192
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
ATG/ATC
AA pos
64
AA ref
M
AA alt
I
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14482C>G
HGNC ID
7462
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot ID
P03923
Uniprot name
NU6M_HUMAN
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-3.832 Conservation Score
PhyloP 470way
-0.165 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.958 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
Neutral 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
Damaging Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
Neutral Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Pathogenic 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
Disease Score and details of the meta-predictor

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
65513
Clinvar ALLELEID
76421
Clinvar CLNDISDB
Mondo:mondo:0044970, medgen:c0751651, orphanet:68380;

human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:104
Clinvar CLNDN
Mitochondrial disease;

leber optic atrophy
Clinvar CLNSIG
Likely pathogenic
MITOMAP Allele
14482C>G
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Cfrm [lp]
MITOMAP Disease Hom/Het
+/+
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
20064630 8742999 18402672 21887510 15972314 29987491 20301353 9443868
MITOMAP Variant Class
disease
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
rs199476108

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
.
~ 14482 (C/A) 14482 (C/G)
~ 14482 (ATG/ATT) 14482 (ATG/ATC)
MitImpact id MI.23786 MI.23787
Chr chrM chrM
Start 14482 14482
Ref C C
Alt A G
Gene symbol MT-ND6 MT-ND6
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6
Gene position 192 192
Gene start 14149 14149
Gene end 14673 14673
Gene strand - -
Codon substitution ATG/ATT ATG/ATC
AA position 64 64
AA ref M M
AA alt I I
Functional effect general missense missense
Functional effect detailed missense missense
OMIM id 516006 516006
HGVS NC_012920.1:g.14482C>A NC_012920.1:g.14482C>G
HGNC id 7462 7462
Respiratory Chain complex I I
Ensembl gene id ENSG00000198695 ENSG00000198695
Ensembl transcript id ENST00000361681 ENST00000361681
Ensembl protein id ENSP00000354665 ENSP00000354665
Uniprot id P03923 P03923
Uniprot name NU6M_HUMAN NU6M_HUMAN
Ncbi gene id 4541 4541
Ncbi protein id YP_003024037.1 YP_003024037.1
PhyloP 100V -3.832 -3.832
PhyloP 470Way -0.165 -0.165
PhastCons 100V 0 0
PhastCons 470Way 0.958 0.958
PolyPhen2 probably_damaging probably_damaging
PolyPhen2 score 0.99 0.99
SIFT neutral neutral
SIFT score 0.31 0.31
SIFT4G Damaging Damaging
SIFT4G score 0.003 0.003
VEST Neutral Neutral
VEST pvalue 0.39 0.39
VEST FDR 0.5 0.5
Mitoclass.1 damaging damaging
SNPDryad Neutral Neutral
SNPDryad score 0.87 0.87
MutationTaster Disease Disease
MutationTaster score 0.99196 0.98444
MutationTaster converted rankscore 0.41520 0.40146
MutationTaster model simple_aae simple_aae
MutationTaster AAE G30C G30R
fathmm Tolerated Tolerated
fathmm score 2.17 2.17
fathmm converted rankscore 0.19020 0.19020
AlphaMissense likely_pathogenic likely_pathogenic
AlphaMissense score 0.8051 0.8051
CADD Deleterious Neutral
CADD score 2.62782 2.126065
CADD phred 20.4 17.02
PROVEAN Tolerated Tolerated
PROVEAN score -1.3 -1.3
MutationAssessor medium medium
MutationAssessor score 2.075 2.075
EFIN SP Damaging Damaging
EFIN SP score 0.186 0.186
EFIN HD Damaging Damaging
EFIN HD score 0.246 0.246
MLC Neutral Neutral
MLC score 0.49508118 0.49508118
PANTHER score 0.19 0.19
PhD-SNP score 0.795 0.795
APOGEE1 Pathogenic Pathogenic
APOGEE1 score 0.96 0.96
APOGEE2 Pathogenic Pathogenic
APOGEE2 score 0.968812523246929 0.968812523246929
CAROL deleterious deleterious
CAROL score 0.99 0.99
Condel neutral neutral
Condel score 0.16 0.16
COVEC WMV deleterious deleterious
COVEC WMV score 1 1
MtoolBox deleterious deleterious
MtoolBox DS 0.79 0.79
DEOGEN2 Tolerated Tolerated
DEOGEN2 score 0.326379 0.326379
DEOGEN2 converted rankscore 0.69700 0.69700
Meta-SNP Disease Disease
Meta-SNP score 0.677 0.677
PolyPhen2 transf low impact low impact
PolyPhen2 transf score -2.63 -2.63
SIFT_transf medium impact medium impact
SIFT transf score 0.01 0.01
MutationAssessor transf medium impact medium impact
MutationAssessor transf score 1.42 1.42
CHASM Neutral Neutral
CHASM pvalue 0.78 0.78
CHASM FDR 0.85 0.85
ClinVar id 9693.0 65513.0
ClinVar Allele id 24732.0 76421.0
ClinVar CLNDISDB MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104 MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104
ClinVar CLNDN Mitochondrial_disease|Leber_optic_atrophy Mitochondrial_disease|Leber_optic_atrophy
ClinVar CLNSIG Likely_pathogenic Likely_pathogenic
MITOMAP Disease Clinical info LHON LHON
MITOMAP Disease Status Cfrm [LP] Cfrm [LP]
MITOMAP Disease Hom/Het +/+ +/+
MITOMAP General GenBank Freq 0.0033% 0.0%
MITOMAP General GenBank Seqs 2 0
MITOMAP General Curated refs 12112086;22879922;12150954;18402672;15972314;19319978;29987491;20301353;16532388;11931086;17122117;21457906;29253894 20064630;8742999;18402672;21887510;15972314;29987491;20301353;9443868
MITOMAP Variant Class disease disease
gnomAD 3.1 AN . .
gnomAD 3.1 AC Homo . .
gnomAD 3.1 AF Hom . .
gnomAD 3.1 AC Het . .
gnomAD 3.1 AF Het . .
gnomAD 3.1 filter . .
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 rs199476108 rs199476108
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