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7623 (C > T)

General info

Mitimpact ID
MI.5254
Chr
chrM
Start
7623
Ref
C
Alt
T
Gene symbol
MT-CO2 Extended gene annotation
Gene position
38
Gene start
7586
Gene end
8269
Gene strand
+
Codon substitution
ACT/ATT
AA pos
13
AA ref
T
AA alt
I
Functional effect
missense
OMIM ID
516040
HGVS
NC_012920.1:g.7623C>T
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
3.164 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0.034 Conservation Score
PhastCons 470way
0.741 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
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
Ambiguous Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Tolerated Score and details of the predictor
Mutation Assessor
Low 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
Deleterious 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
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Neutral 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
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
1684905
Clinvar ALLELEID
1676930
Clinvar CLNDISDB
Medgen:cn169374
Clinvar CLNDN
Not specified
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
7623C>T
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
17003408
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56433
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
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.2511
HelixMTdb max ARF
0.2511
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs2124594114

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
.

7623 (C > A)

General info

Mitimpact ID
MI.5253
Chr
chrM
Start
7623
Ref
C
Alt
A
Gene symbol
MT-CO2 Extended gene annotation
Gene position
38
Gene start
7586
Gene end
8269
Gene strand
+
Codon substitution
ACT/AAT
AA pos
13
AA ref
T
AA alt
N
Functional effect
missense
OMIM ID
516040
HGVS
NC_012920.1:g.7623C>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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Powered by MitoWheel

Conservation

PhyloP 100v
3.164 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0.034 Conservation Score
PhastCons 470way
0.741 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
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
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Neutral 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
Deleterious 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
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Neutral 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
Low 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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
7623C>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
.

7623 (C > G)

General info

Mitimpact ID
MI.5255
Chr
chrM
Start
7623
Ref
C
Alt
G
Gene symbol
MT-CO2 Extended gene annotation
Gene position
38
Gene start
7586
Gene end
8269
Gene strand
+
Codon substitution
ACT/AGT
AA pos
13
AA ref
T
AA alt
S
Functional effect
missense
OMIM ID
516040
HGVS
NC_012920.1:g.7623C>G
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
3.164 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0.034 Conservation Score
PhastCons 470way
0.741 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
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
Deleterious 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
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Neutral 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
Low 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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
7623C>G
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
.
~ 7623 (C/T) 7623 (C/A) 7623 (C/G)
~ 7623 (ACT/ATT) 7623 (ACT/AAT) 7623 (ACT/AGT)
MitImpact id MI.5254 MI.5253 MI.5255
Chr chrM chrM chrM
Start 7623 7623 7623
Ref C C C
Alt T A G
Gene symbol MT-CO2 MT-CO2 MT-CO2
Extended annotation mitochondrially encoded cytochrome c oxidase II mitochondrially encoded cytochrome c oxidase II mitochondrially encoded cytochrome c oxidase II
Gene position 38 38 38
Gene start 7586 7586 7586
Gene end 8269 8269 8269
Gene strand + + +
Codon substitution ACT/ATT ACT/AAT ACT/AGT
AA position 13 13 13
AA ref T T T
AA alt I N S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516040 516040 516040
HGVS NC_012920.1:g.7623C>T NC_012920.1:g.7623C>A NC_012920.1:g.7623C>G
HGNC id 7421 7421 7421
Respiratory Chain complex IV IV IV
Ensembl gene id ENSG00000198712 ENSG00000198712 ENSG00000198712
Ensembl transcript id ENST00000361739 ENST00000361739 ENST00000361739
Ensembl protein id ENSP00000354876 ENSP00000354876 ENSP00000354876
Uniprot id P00403 P00403 P00403
Uniprot name COX2_HUMAN COX2_HUMAN COX2_HUMAN
Ncbi gene id 4513 4513 4513
Ncbi protein id YP_003024029.1 YP_003024029.1 YP_003024029.1
PhyloP 100V 3.164 3.164 3.164
PhyloP 470Way 0.65 0.65 0.65
PhastCons 100V 0.034 0.034 0.034
PhastCons 470Way 0.741 0.741 0.741
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0 0.99
SIFT neutral neutral neutral
SIFT score 0.32 0.58 0.76
SIFT4G Damaging Damaging Tolerated
SIFT4G score 0.027 0.048 0.247
VEST Neutral Neutral Neutral
VEST pvalue 0.31 0.47 0.49
VEST FDR 0.45 0.55 0.55
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.84 0.82 0.32
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 0.999999 0.999999 1
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE T13I T13N T13S
fathmm Tolerated Tolerated Tolerated
fathmm score 1.51 1.62 1.78
fathmm converted rankscore 0.30937 0.28189 0.25678
AlphaMissense ambiguous likely_benign likely_benign
AlphaMissense score 0.3665 0.2539 0.134
CADD Deleterious Deleterious Neutral
CADD score 3.635305 3.260152 0.234792
CADD phred 23.2 22.8 5.042
PROVEAN Tolerated Damaging Tolerated
PROVEAN score -1.96 -2.54 -0.41
MutationAssessor low neutral neutral
MutationAssessor score 1.58 0.385 0.115
EFIN SP Damaging Damaging Neutral
EFIN SP score 0.534 0.542 0.722
EFIN HD Damaging Damaging Neutral
EFIN HD score 0.198 0.17 0.622
MLC Deleterious Deleterious Deleterious
MLC score 0.52649526 0.52649526 0.52649526
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.46 0.28 0.31
APOGEE2 Likely-benign Likely-benign Benign
APOGEE2 score 0.202940863450042 0.186809070675086 0.0457665007522723
CAROL deleterious deleterious deleterious
CAROL score 1.0 1.0 0.99
Condel neutral neutral neutral
Condel score 0.16 0.29 0.39
COVEC WMV neutral neutral neutral
COVEC WMV score -2 -2 -2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.77 0.75 0.71
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.023808 0.077062 0.004267
DEOGEN2 converted rankscore 0.18107 0.35566 0.03680
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.52 -3.52 -2.58
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.02 0.28 0.48
MutationAssessor transf medium impact low impact low impact
MutationAssessor transf score 0.12 -1.11 -1.46
CHASM Neutral Neutral Neutral
CHASM pvalue 0.49 0.56 0.44
CHASM FDR 0.8 0.8 0.8
ClinVar id 1684905.0 . .
ClinVar Allele id 1676930.0 . .
ClinVar CLNDISDB MedGen:CN169374 . .
ClinVar CLNDN not_specified . .
ClinVar CLNSIG Uncertain_significance . .
MITOMAP Disease Clinical info LHON . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.0% . .
MITOMAP General GenBank Seqs 0 . .
MITOMAP General Curated refs 17003408 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56433.0 . .
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 0.0 . .
HelixMTdb AF Hom 0.0 . .
HelixMTdb AC Het 1.0 . .
HelixMTdb AF Het 5.1024836e-06 . .
HelixMTdb mean ARF 0.2511 . .
HelixMTdb max ARF 0.2511 . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs2124594114 . .
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