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9682 (T > C)

General info

Mitimpact ID
MI.7641
Chr
chrM
Start
9682
Ref
T
Alt
C
Gene symbol
MT-CO3 Extended gene annotation
Gene position
476
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
ATA/ACA
AA pos
159
AA ref
M
AA alt
T
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9682T>C
HGNC ID
7422
RC complex
IV
Ensembl gene ID
ENSG00000198938
Ensembl protein ID
ENSP00000354982
Ensembl transcript ID
ENST00000362079
Uniprot ID
P00414
Uniprot name
COX3_HUMAN
Ncbi gene ID
4514
Ncbi protein ID
YP_003024032.1
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Conservation

PhyloP 100v
1.211 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0.002 Conservation Score
PhastCons 470way
0.26 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
.
fathmm
.
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
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
High impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Low 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
693205
Clinvar ALLELEID
681741
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
9682T>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.139%
MITOMAP General GenBank Seqs
85
MITOMAP General GenBank Curated refs
21978175 24467713 11938495 12509511 12840039 15791543 16172508
MITOMAP Variant Class
polymorphism
Gnomad AN
56425
Gnomad AC hom
791
Gnomad AF hom
0.0140186
Gnomad AC het
5
Gnomad AF het
8.86e-05
Gnomad filter
Pass
HelixMTdb AC hom
614
HelixMTdb AF hom
0.0031329
HelixMTdb AC het
6
HelixMTdb AF het
3.06e-05
HelixMTdb mean ARF
0.63829
HelixMTdb max ARF
0.77512
ToMMo JPN54K AC
9
ToMMo JPN54K AF
0.000166
ToMMo JPN54K AN
54302
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
.

9682 (T > A)

General info

Mitimpact ID
MI.7642
Chr
chrM
Start
9682
Ref
T
Alt
A
Gene symbol
MT-CO3 Extended gene annotation
Gene position
476
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
ATA/AAA
AA pos
159
AA ref
M
AA alt
K
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9682T>A
HGNC ID
7422
RC complex
IV
Ensembl gene ID
ENSG00000198938
Ensembl protein ID
ENSP00000354982
Ensembl transcript ID
ENST00000362079
Uniprot ID
P00414
Uniprot name
COX3_HUMAN
Ncbi gene ID
4514
Ncbi protein ID
YP_003024032.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
1.211 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0.002 Conservation Score
PhastCons 470way
0.26 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Pathogenic Score and details of the predictor
MitoClass 1
Neutral Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
.
fathmm
.
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
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
.
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
9682T>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
.
~ 9682 (T/C) 9682 (T/A)
~ 9682 (ATA/ACA) 9682 (ATA/AAA)
MitImpact id MI.7641 MI.7642
Chr chrM chrM
Start 9682 9682
Ref T T
Alt C A
Gene symbol MT-CO3 MT-CO3
Extended annotation mitochondrially encoded cytochrome c oxidase III mitochondrially encoded cytochrome c oxidase III
Gene position 476 476
Gene start 9207 9207
Gene end 9990 9990
Gene strand + +
Codon substitution ATA/ACA ATA/AAA
AA position 159 159
AA ref M M
AA alt T K
Functional effect general missense missense
Functional effect detailed missense missense
OMIM id 516050 516050
HGVS NC_012920.1:g.9682T>C NC_012920.1:g.9682T>A
HGNC id 7422 7422
Respiratory Chain complex IV IV
Ensembl gene id ENSG00000198938 ENSG00000198938
Ensembl transcript id ENST00000362079 ENST00000362079
Ensembl protein id ENSP00000354982 ENSP00000354982
Uniprot id P00414 P00414
Uniprot name COX3_HUMAN COX3_HUMAN
Ncbi gene id 4514 4514
Ncbi protein id YP_003024032.1 YP_003024032.1
PhyloP 100V 1.211 1.211
PhyloP 470Way 0.666 0.666
PhastCons 100V 0.002 0.002
PhastCons 470Way 0.26 0.26
PolyPhen2 benign benign
PolyPhen2 score 0.0 0.05
SIFT neutral neutral
SIFT score 0.65 0.47
SIFT4G Tolerated Damaging
SIFT4G score 0.421 0.004
VEST Neutral Pathogenic
VEST pvalue 0.13 0.03
VEST FDR 0.4 0.35
Mitoclass.1 neutral neutral
SNPDryad Neutral Pathogenic
SNPDryad score 0.51 0.95
MutationTaster . .
MutationTaster score . .
MutationTaster converted rankscore . .
MutationTaster model . .
MutationTaster AAE . .
fathmm . .
fathmm score . .
fathmm converted rankscore . .
AlphaMissense likely_benign likely_pathogenic
AlphaMissense score 0.148 0.8866
CADD Neutral Neutral
CADD score -0.415395 2.342562
CADD phred 0.355 18.45
PROVEAN Tolerated Tolerated
PROVEAN score 1.17 -0.88
MutationAssessor neutral medium
MutationAssessor score -0.885 2.845
EFIN SP Neutral Damaging
EFIN SP score 0.784 0.584
EFIN HD Neutral Neutral
EFIN HD score 0.798 0.412
MLC Neutral Neutral
MLC score 0.28351138 0.28351138
PANTHER score . .
PhD-SNP score . .
APOGEE1 Neutral Neutral
APOGEE1 score 0.23 0.34
APOGEE2 Benign Likely-benign
APOGEE2 score 0.0315833974242117 0.218759461182717
CAROL neutral neutral
CAROL score 0.34 0.48
Condel deleterious deleterious
Condel score 0.83 0.71
COVEC WMV neutral neutral
COVEC WMV score -6 -6
MtoolBox neutral neutral
MtoolBox DS 0.14 0.26
DEOGEN2 . .
DEOGEN2 score . .
DEOGEN2 converted rankscore . .
Meta-SNP . .
Meta-SNP score . .
PolyPhen2 transf high impact medium impact
PolyPhen2 transf score 2.05 0.37
SIFT_transf medium impact medium impact
SIFT transf score 0.35 0.16
MutationAssessor transf low impact medium impact
MutationAssessor transf score -2.03 -0.06
CHASM Neutral Neutral
CHASM pvalue 0.17 0.21
CHASM FDR 0.8 0.8
ClinVar id 693205.0 .
ClinVar Allele id 681741.0 .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 .
ClinVar CLNDN Leigh_syndrome .
ClinVar CLNSIG Benign .
MITOMAP Disease Clinical info . .
MITOMAP Disease Status . .
MITOMAP Disease Hom/Het ./. ./.
MITOMAP General GenBank Freq 0.139% .
MITOMAP General GenBank Seqs 85 .
MITOMAP General Curated refs 21978175;24467713;11938495;12509511;12840039;15791543;16172508 .
MITOMAP Variant Class polymorphism .
gnomAD 3.1 AN 56425.0 .
gnomAD 3.1 AC Homo 791.0 .
gnomAD 3.1 AF Hom 0.0140186 .
gnomAD 3.1 AC Het 5.0 .
gnomAD 3.1 AF Het 8.86132e-05 .
gnomAD 3.1 filter PASS .
HelixMTdb AC Hom 614.0 .
HelixMTdb AF Hom 0.003132925 .
HelixMTdb AC Het 6.0 .
HelixMTdb AF Het 3.06149e-05 .
HelixMTdb mean ARF 0.63829 .
HelixMTdb max ARF 0.77512 .
ToMMo 54KJPN AC 9 .
ToMMo 54KJPN AF 0.000166 .
ToMMo 54KJPN AN 54302 .
COSMIC 90 . .
dbSNP 156 id . .
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