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7671 (T > A)

General info

Mitimpact ID
MI.5365
Chr
chrM
Start
7671
Ref
T
Alt
A
Gene symbol
MT-CO2 Extended gene annotation
Gene position
86
Gene start
7586
Gene end
8269
Gene strand
+
Codon substitution
ATA/AAA
AA pos
29
AA ref
M
AA alt
K
Functional effect
missense
OMIM ID
516040
HGVS
NC_012920.1:g.7671T>A
HGNC ID
7421
RC complex
IV
Ensembl gene ID
ENSG00000198712
Ensembl protein ID
ENSP00000354876
Ensembl transcript ID
ENST00000361739
Uniprot ID
P00403
Uniprot name
COX2_HUMAN
Ncbi gene ID
4513
Ncbi protein ID
YP_003024029.1
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Conservation

PhyloP 100v
4.822 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.267 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
Pathogenic Score and details of the predictor
MutationTaster
.
fathmm
.
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
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
.
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
.
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
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
9660
Clinvar ALLELEID
24699
Clinvar CLNDISDB
Mondo:mondo:0009068, medgen:c5435656, omim:220110, orphanet:254905
Clinvar CLNDN
Cytochrome-c oxidase deficiency disease
Clinvar CLNSIG
Pathogenic
MITOMAP Allele
7671T>A
MITOMAP Disease Clinical info
Mm
MITOMAP Disease Status
Reported [vus]
MITOMAP Disease Hom/Het
-/+
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
21457906 10486321
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
.

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
.

7671 (T > C)

General info

Mitimpact ID
MI.5364
Chr
chrM
Start
7671
Ref
T
Alt
C
Gene symbol
MT-CO2 Extended gene annotation
Gene position
86
Gene start
7586
Gene end
8269
Gene strand
+
Codon substitution
ATA/ACA
AA pos
29
AA ref
M
AA alt
T
Functional effect
missense
OMIM ID
516040
HGVS
NC_012920.1:g.7671T>C
HGNC ID
7421
RC complex
IV
Ensembl gene ID
ENSG00000198712
Ensembl protein ID
ENSP00000354876
Ensembl transcript ID
ENST00000361739
Uniprot ID
P00403
Uniprot name
COX2_HUMAN
Ncbi gene ID
4513
Ncbi protein ID
YP_003024029.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
4.822 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.267 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
Pathogenic 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
Damaging 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
.
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
.
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
7671T>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
56432
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
.

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
.
~ 7671 (T/A) 7671 (T/C)
~ 7671 (ATA/AAA) 7671 (ATA/ACA)
MitImpact id MI.5365 MI.5364
Chr chrM chrM
Start 7671 7671
Ref T T
Alt A C
Gene symbol MT-CO2 MT-CO2
Extended annotation mitochondrially encoded cytochrome c oxidase II mitochondrially encoded cytochrome c oxidase II
Gene position 86 86
Gene start 7586 7586
Gene end 8269 8269
Gene strand + +
Codon substitution ATA/AAA ATA/ACA
AA position 29 29
AA ref M M
AA alt K T
Functional effect general missense missense
Functional effect detailed missense missense
OMIM id 516040 516040
HGVS NC_012920.1:g.7671T>A NC_012920.1:g.7671T>C
HGNC id 7421 7421
Respiratory Chain complex IV IV
Ensembl gene id ENSG00000198712 ENSG00000198712
Ensembl transcript id ENST00000361739 ENST00000361739
Ensembl protein id ENSP00000354876 ENSP00000354876
Uniprot id P00403 P00403
Uniprot name COX2_HUMAN COX2_HUMAN
Ncbi gene id 4513 4513
Ncbi protein id YP_003024029.1 YP_003024029.1
PhyloP 100V 4.822 4.822
PhyloP 470Way 0.666 0.666
PhastCons 100V 1 1
PhastCons 470Way 0.267 0.267
PolyPhen2 probably_damaging probably_damaging
PolyPhen2 score 0.95 0.98
SIFT neutral neutral
SIFT score 0.11 0.22
SIFT4G Damaging Damaging
SIFT4G score 0.0 0.035
VEST Neutral Neutral
VEST pvalue 0.19 0.3
VEST FDR 0.45 0.45
Mitoclass.1 damaging damaging
SNPDryad Pathogenic Pathogenic
SNPDryad score 1.0 0.92
MutationTaster . .
MutationTaster score . .
MutationTaster converted rankscore . .
MutationTaster model . .
MutationTaster AAE . .
fathmm . .
fathmm score . .
fathmm converted rankscore . .
AlphaMissense likely_pathogenic ambiguous
AlphaMissense score 0.916 0.5402
CADD Deleterious Deleterious
CADD score 3.789753 2.750668
CADD phred 23.4 21.1
PROVEAN Damaging Damaging
PROVEAN score -5.5 -5.13
MutationAssessor high medium
MutationAssessor score 4.72 2.005
EFIN SP Damaging Damaging
EFIN SP score 0.066 0.184
EFIN HD Damaging Damaging
EFIN HD score 0.014 0.092
MLC Neutral Neutral
MLC score 0.09360855 0.09360855
PANTHER score . .
PhD-SNP score 0.738 .
APOGEE1 Pathogenic Pathogenic
APOGEE1 score 0.9 0.85
APOGEE2 Pathogenic VUS
APOGEE2 score 0.942437283550845 0.528169897706611
CAROL deleterious deleterious
CAROL score 0.98 0.98
Condel neutral neutral
Condel score 0.08 0.12
COVEC WMV deleterious deleterious
COVEC WMV score 2 1
MtoolBox deleterious deleterious
MtoolBox DS 0.86 0.81
DEOGEN2 . .
DEOGEN2 score . .
DEOGEN2 converted rankscore . .
Meta-SNP Disease .
Meta-SNP score 0.821 .
PolyPhen2 transf low impact low impact
PolyPhen2 transf score -1.91 -2.3
SIFT_transf medium impact medium impact
SIFT transf score -0.3 -0.1
MutationAssessor transf high impact medium impact
MutationAssessor transf score 2.63 1.12
CHASM Neutral Neutral
CHASM pvalue 0.38 0.3
CHASM FDR 0.8 0.8
ClinVar id 9660.0 .
ClinVar Allele id 24699.0 .
ClinVar CLNDISDB MONDO:MONDO:0009068,MedGen:C5435656,OMIM:220110,Orphanet:254905 .
ClinVar CLNDN Cytochrome-c_oxidase_deficiency_disease .
ClinVar CLNSIG Pathogenic .
MITOMAP Disease Clinical info MM .
MITOMAP Disease Status Reported [VUS] .
MITOMAP Disease Hom/Het -/+ ./.
MITOMAP General GenBank Freq 0.0% .
MITOMAP General GenBank Seqs 0 .
MITOMAP General Curated refs 21457906;10486321 .
MITOMAP Variant Class disease .
gnomAD 3.1 AN . 56432.0
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 . .
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