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14279 (G > A)

General info

Mitimpact ID
MI.23368
Chr
chrM
Start
14279
Ref
G
Alt
A
Gene symbol
MT-ND6 Extended gene annotation
Gene position
395
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
TCA/TTA
AA pos
132
AA ref
S
AA alt
L
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14279G>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
0.385 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.008 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
Neutral 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
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
65516
Clinvar ALLELEID
76424
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

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

leber optic atrophy
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
14279G>A
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.0115%
MITOMAP General GenBank Seqs
7
MITOMAP General GenBank Curated refs
26735972 15922297 29987491 20301353 19047048 18806273 32652755
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56417
Gnomad AC hom
3
Gnomad AF hom
5.31e-05
Gnomad AC het
4
Gnomad AF het
7.09e-05
Gnomad filter
Pass
HelixMTdb AC hom
5
HelixMTdb AF hom
2.55e-05
HelixMTdb AC het
27
HelixMTdb AF het
0.0001377
HelixMTdb mean ARF
0.30727
HelixMTdb max ARF
0.88372
ToMMo JPN54K AC
1
ToMMo JPN54K AF
1.8e-05
ToMMo JPN54K AN
54302
COSMIC 90
COSM6716818
dbSNP 156
rs869025187

Residue interaction

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

Compensated Pathogenic Deviations

Frequency
1.34 CPD variant frequency
AA ref
S
CPD AA alt
L
Aln pos
143
RefSeq protein ID
YP_008378980 , YP_009024903 , YP_007183099 , YP_007316933 , YP_003331234 , NP_149968 , YP_006576332 , YP_009019451
Species name
Erythrocebus patas, Cercopithecus diana, Theropithecus gelada, Papio papio, Eothenomys chinensis, Microtus kikuchii, Marmota himalayana, Ratufa bicolor
Ncbi taxon ID
9538, 36224, 9565, 100937, 577681, 100899, 93163, 226822

14279 (G > C)

General info

Mitimpact ID
MI.23367
Chr
chrM
Start
14279
Ref
G
Alt
C
Gene symbol
MT-ND6 Extended gene annotation
Gene position
395
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
TCA/TGA
AA pos
132
AA ref
S
AA alt
W
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14279G>C
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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Powered by MitoWheel

Conservation

PhyloP 100v
0.385 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.008 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging 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
.
fathmm
.
AlphaMissense
Likely benign 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
Deleterious Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
.
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
14279G>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
56432
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
1
HelixMTdb AF hom
5.1e-06
HelixMTdb AC het
0
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

Residue interaction

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

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.
~ 14279 (G/A) 14279 (G/C)
~ 14279 (TCA/TTA) 14279 (TCA/TGA)
MitImpact id MI.23368 MI.23367
Chr chrM chrM
Start 14279 14279
Ref G G
Alt A C
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 395 395
Gene start 14149 14149
Gene end 14673 14673
Gene strand - -
Codon substitution TCA/TTA TCA/TGA
AA position 132 132
AA ref S S
AA alt L W
Functional effect general missense missense
Functional effect detailed missense missense
OMIM id 516006 516006
HGVS NC_012920.1:g.14279G>A NC_012920.1:g.14279G>C
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 0.385 0.385
PhyloP 470Way 0.458 0.458
PhastCons 100V 0 0
PhastCons 470Way 0.008 0.008
PolyPhen2 benign probably_damaging
PolyPhen2 score 0.01 0.91
SIFT neutral neutral
SIFT score 0.65 0.18
SIFT4G Tolerated Tolerated
SIFT4G score 0.653 0.185
VEST Neutral Neutral
VEST pvalue 0.28 0.27
VEST FDR 0.45 0.45
Mitoclass.1 neutral neutral
SNPDryad Neutral Neutral
SNPDryad score 0.58 0.73
MutationTaster Polymorphism .
MutationTaster score 1 .
MutationTaster converted rankscore 0.08975 .
MutationTaster model without_aae .
MutationTaster AAE . .
fathmm Tolerated .
fathmm score 1.63 .
fathmm converted rankscore 0.28002 .
AlphaMissense likely_benign likely_benign
AlphaMissense score 0.0928 0.241
CADD Neutral Deleterious
CADD score 0.384061 2.864351
CADD phred 6.474 21.7
PROVEAN Tolerated Tolerated
PROVEAN score -0.21 -2.33
MutationAssessor neutral .
MutationAssessor score 0.26 .
EFIN SP Neutral Neutral
EFIN SP score 0.906 0.77
EFIN HD Neutral Neutral
EFIN HD score 0.956 0.79
MLC Neutral Neutral
MLC score 0.20037419 0.20037419
PANTHER score . .
PhD-SNP score . .
APOGEE1 Neutral Neutral
APOGEE1 score 0.42 0.32
APOGEE2 Benign VUS-
APOGEE2 score 0.0600996524766674 0.352108924155894
CAROL neutral neutral
CAROL score 0.33 0.95
Condel deleterious neutral
Condel score 0.82 0.14
COVEC WMV neutral deleterious
COVEC WMV score -6 1
MtoolBox neutral deleterious
MtoolBox DS 0.16 0.75
DEOGEN2 Tolerated .
DEOGEN2 score 0.175011 .
DEOGEN2 converted rankscore 0.52445 .
Meta-SNP . .
Meta-SNP score . .
PolyPhen2 transf medium impact low impact
PolyPhen2 transf score 1.03 -1.72
SIFT_transf medium impact medium impact
SIFT transf score 0.36 -0.16
MutationAssessor transf medium impact medium impact
MutationAssessor transf score -0.5 0.53
CHASM Neutral Neutral
CHASM pvalue 0.82 0.58
CHASM FDR 0.85 0.8
ClinVar id 65516.0 .
ClinVar Allele id 76424.0 .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104 .
ClinVar CLNDN Leigh_syndrome|Leber_optic_atrophy .
ClinVar CLNSIG Uncertain_significance .
MITOMAP Disease Clinical info LHON .
MITOMAP Disease Status Reported .
MITOMAP Disease Hom/Het +/- ./.
MITOMAP General GenBank Freq 0.0115% 0.0016%
MITOMAP General GenBank Seqs 7 1
MITOMAP General Curated refs 26735972;15922297;29987491;20301353;19047048;18806273;32652755 .
MITOMAP Variant Class polymorphism;disease polymorphism
gnomAD 3.1 AN 56417.0 56432.0
gnomAD 3.1 AC Homo 3.0 0.0
gnomAD 3.1 AF Hom 5.31755e-05 0.0
gnomAD 3.1 AC Het 4.0 1.0
gnomAD 3.1 AF Het 7.09006e-05 1.77204e-05
gnomAD 3.1 filter PASS PASS
HelixMTdb AC Hom 5.0 1.0
HelixMTdb AF Hom 2.5512418e-05 5.1024836e-06
HelixMTdb AC Het 27.0 0.0
HelixMTdb AF Het 0.00013776706 0.0
HelixMTdb mean ARF 0.30727 .
HelixMTdb max ARF 0.88372 .
ToMMo 54KJPN AC 1 .
ToMMo 54KJPN AF 1.8e-05 .
ToMMo 54KJPN AN 54302 .
COSMIC 90 COSM6716818 .
dbSNP 156 id rs869025187 .
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