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7587 (T > C)

General info

Mitimpact ID
MI.5176
Chr
chrM
Start
7587
Ref
T
Alt
C
Gene symbol
MT-CO2 Extended gene annotation
Gene position
2
Gene start
7586
Gene end
8269
Gene strand
+
Codon substitution
ATG/ACG
AA pos
1
AA ref
M
AA alt
T
Functional effect
start_lost
OMIM ID
516040
HGVS
NC_012920.1:g.7587T>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
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Conservation

PhyloP 100v
7.73 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.14 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
Disease automatic Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
.
CADD
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
.
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
MLC
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-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
.

Cancer-specific predictors

PolyPhen2 transf
.
SIFT transf
.
MutationAssessor transf
.
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
9658
Clinvar ALLELEID
24697
Clinvar CLNDISDB
Mondo:mondo:0009068, medgen:c5435656, omim:220110, orphanet:254905
Clinvar CLNDN
Cytochrome-c oxidase deficiency disease
Clinvar CLNSIG
Pathogenic
MITOMAP Allele
7587T>C
MITOMAP Disease Clinical info
Mitochondrial encephalomyopathy
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
21457906 10205264
MITOMAP Variant Class
disease
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
rs199474825

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
.

7587 (T > A)

General info

Mitimpact ID
MI.5175
Chr
chrM
Start
7587
Ref
T
Alt
A
Gene symbol
MT-CO2 Extended gene annotation
Gene position
2
Gene start
7586
Gene end
8269
Gene strand
+
Codon substitution
ATG/AAG
AA pos
1
AA ref
M
AA alt
K
Functional effect
start_lost
OMIM ID
516040
HGVS
NC_012920.1:g.7587T>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.73 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.14 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
Disease Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
.
CADD
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
.
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
MLC
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-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
.

Cancer-specific predictors

PolyPhen2 transf
.
SIFT transf
.
MutationAssessor transf
.
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
7587T>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
.
~ 7587 (T/C) 7587 (T/A)
~ 7587 (ATG/ACG) 7587 (ATG/AAG)
MitImpact id MI.5176 MI.5175
Chr chrM chrM
Start 7587 7587
Ref T T
Alt C A
Gene symbol MT-CO2 MT-CO2
Extended annotation mitochondrially encoded cytochrome c oxidase II mitochondrially encoded cytochrome c oxidase II
Gene position 2 2
Gene start 7586 7586
Gene end 8269 8269
Gene strand + +
Codon substitution ATG/ACG ATG/AAG
AA position 1 1
AA ref M M
AA alt T K
Functional effect general start_lost start_lost
Functional effect detailed start_lost start_lost
OMIM id 516040 516040
HGVS NC_012920.1:g.7587T>C NC_012920.1:g.7587T>A
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 7.73 7.73
PhyloP 470Way 0.666 0.666
PhastCons 100V 1 1
PhastCons 470Way 0.14 0.14
PolyPhen2 probably_damaging probably_damaging
PolyPhen2 score 0.97 0.97
SIFT deleterious deleterious
SIFT score 0.0 0.0
SIFT4G Damaging Damaging
SIFT4G score 0.0 0.0
VEST Neutral Neutral
VEST pvalue 0.37 0.3
VEST FDR 0.5 0.45
Mitoclass.1 damaging damaging
SNPDryad Pathogenic Pathogenic
SNPDryad score 0.92 1.0
MutationTaster Disease automatic Disease
MutationTaster score 1 1
MutationTaster converted rankscore 0.81001 0.81001
MutationTaster model complex_aae complex_aae
MutationTaster AAE A2Q A2Q
fathmm Tolerated Tolerated
fathmm score 1.24 1.27
fathmm converted rankscore 0.36691 0.36146
AlphaMissense . .
AlphaMissense score . .
CADD Deleterious Deleterious
CADD score 2.728718 3.800415
CADD phred 21.0 23.4
PROVEAN Damaging Damaging
PROVEAN score -5.73 -5.73
MutationAssessor . .
MutationAssessor score . .
EFIN SP Damaging Damaging
EFIN SP score 0.156 0.148
EFIN HD Damaging Damaging
EFIN HD score 0.016 0.014
MLC Deleterious Deleterious
MLC score 0.7 0.7
PANTHER score . .
PhD-SNP score . .
APOGEE1 Pathogenic Pathogenic
APOGEE1 score 0.79 0.83
APOGEE2 Likely-pathogenic Likely-pathogenic
APOGEE2 score 0.875036505601518 0.804333931513274
CAROL deleterious deleterious
CAROL score 1.0 1.0
Condel neutral neutral
Condel score 0.02 0.02
COVEC WMV deleterious deleterious
COVEC WMV score 4 4
MtoolBox deleterious deleterious
MtoolBox DS 0.79 0.79
DEOGEN2 Tolerated Tolerated
DEOGEN2 score 0.231232 0.129293
DEOGEN2 converted rankscore 0.59750 0.45748
Meta-SNP . .
Meta-SNP score . .
PolyPhen2 transf . .
PolyPhen2 transf score . .
SIFT_transf . .
SIFT transf score . .
MutationAssessor transf . .
MutationAssessor transf score . .
CHASM Neutral Neutral
CHASM pvalue 0.22 0.36
CHASM FDR 0.8 0.8
ClinVar id 9658.0 .
ClinVar Allele id 24697.0 .
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 Mitochondrial Encephalomyopathy .
MITOMAP Disease Status Cfrm [LP] .
MITOMAP Disease Hom/Het -/+ ./.
MITOMAP General GenBank Freq 0.0% .
MITOMAP General GenBank Seqs 0 .
MITOMAP General Curated refs 21457906;10205264 .
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 rs199474825 .
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