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5961 (C > A)

General info

Mitimpact ID
MI.2000
Chr
chrM
Start
5961
Ref
C
Alt
A
Gene symbol
MT-CO1 Extended gene annotation
Gene position
58
Gene start
5904
Gene end
7445
Gene strand
+
Codon substitution
CTA/ATA
AA pos
20
AA ref
L
AA alt
M
Functional effect
missense
OMIM ID
516030
HGVS
NC_012920.1:g.5961C>A
HGNC ID
7419
RC complex
IV
Ensembl gene ID
ENSG00000198804
Ensembl protein ID
ENSP00000354499
Ensembl transcript ID
ENST00000361624
Uniprot ID
P00395
Uniprot name
COX1_HUMAN
Ncbi gene ID
4512
Ncbi protein ID
YP_003024028.1
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Conservation

PhyloP 100v
-2.488 Conservation Score
PhyloP 470way
-0.997 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.002 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
Damaging 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
.
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
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
.
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
692602
Clinvar ALLELEID
681138
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
5961C>A
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
56434
Gnomad AC hom
5
Gnomad AF hom
8.85e-05
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
2
HelixMTdb AF hom
1.02e-05
HelixMTdb AC het
0
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
1
ToMMo JPN54K AF
1.8e-05
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
.

5961 (C > G)

General info

Mitimpact ID
MI.2001
Chr
chrM
Start
5961
Ref
C
Alt
G
Gene symbol
MT-CO1 Extended gene annotation
Gene position
58
Gene start
5904
Gene end
7445
Gene strand
+
Codon substitution
CTA/GTA
AA pos
20
AA ref
L
AA alt
V
Functional effect
missense
OMIM ID
516030
HGVS
NC_012920.1:g.5961C>G
HGNC ID
7419
RC complex
IV
Ensembl gene ID
ENSG00000198804
Ensembl protein ID
ENSP00000354499
Ensembl transcript ID
ENST00000361624
Uniprot ID
P00395
Uniprot name
COX1_HUMAN
Ncbi gene ID
4512
Ncbi protein ID
YP_003024028.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-2.488 Conservation Score
PhyloP 470way
-0.997 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.002 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
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
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
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
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
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
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
5961C>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
.
~ 5961 (C/A) 5961 (C/G)
~ 5961 (CTA/ATA) 5961 (CTA/GTA)
MitImpact id MI.2000 MI.2001
Chr chrM chrM
Start 5961 5961
Ref C C
Alt A G
Gene symbol MT-CO1 MT-CO1
Extended annotation mitochondrially encoded cytochrome c oxidase I mitochondrially encoded cytochrome c oxidase I
Gene position 58 58
Gene start 5904 5904
Gene end 7445 7445
Gene strand + +
Codon substitution CTA/ATA CTA/GTA
AA position 20 20
AA ref L L
AA alt M V
Functional effect general missense missense
Functional effect detailed missense missense
OMIM id 516030 516030
HGVS NC_012920.1:g.5961C>A NC_012920.1:g.5961C>G
HGNC id 7419 7419
Respiratory Chain complex IV IV
Ensembl gene id ENSG00000198804 ENSG00000198804
Ensembl transcript id ENST00000361624 ENST00000361624
Ensembl protein id ENSP00000354499 ENSP00000354499
Uniprot id P00395 P00395
Uniprot name COX1_HUMAN COX1_HUMAN
Ncbi gene id 4512 4512
Ncbi protein id YP_003024028.1 YP_003024028.1
PhyloP 100V -2.488 -2.488
PhyloP 470Way -0.997 -0.997
PhastCons 100V 0 0
PhastCons 470Way 0.002 0.002
PolyPhen2 probably_damaging probably_damaging
PolyPhen2 score 1.0 0.99
SIFT neutral deleterious
SIFT score 0.08 0.01
SIFT4G Tolerated Damaging
SIFT4G score 0.072 0.012
VEST Neutral Neutral
VEST pvalue 0.19 0.17
VEST FDR 0.55 0.55
Mitoclass.1 damaging damaging
SNPDryad Neutral Neutral
SNPDryad score 0.59 0.66
MutationTaster . Polymorphism
MutationTaster score . 0.999103
MutationTaster converted rankscore . 0.21619
MutationTaster model . simple_aae
MutationTaster AAE . L20V
fathmm . Tolerated
fathmm score . 2.73
fathmm converted rankscore . 0.11839
AlphaMissense likely_benign ambiguous
AlphaMissense score 0.3143 0.5034
CADD Neutral Neutral
CADD score 0.929333 1.521505
CADD phred 10.25 13.43
PROVEAN Tolerated Tolerated
PROVEAN score -0.29 -0.71
MutationAssessor . medium
MutationAssessor score . 2.795
EFIN SP Neutral Neutral
EFIN SP score 0.718 0.624
EFIN HD Neutral Neutral
EFIN HD score 0.84 0.454
MLC Deleterious Deleterious
MLC score 0.84824069 0.84824069
PANTHER score . .
PhD-SNP score . .
APOGEE1 Neutral Neutral
APOGEE1 score 0.44 0.36
APOGEE2 Likely-benign Likely-benign
APOGEE2 score 0.141258963013312 0.222374749782935
CAROL deleterious deleterious
CAROL score 1.0 1.0
Condel neutral neutral
Condel score 0.04 0.01
COVEC WMV neutral deleterious
COVEC WMV score -2 5
MtoolBox deleterious deleterious
MtoolBox DS 0.78 0.79
DEOGEN2 . Tolerated
DEOGEN2 score . 0.029003
DEOGEN2 converted rankscore . 0.20880
Meta-SNP . .
Meta-SNP score . .
PolyPhen2 transf low impact low impact
PolyPhen2 transf score -3.58 -2.64
SIFT_transf medium impact medium impact
SIFT transf score -0.4 -0.92
MutationAssessor transf medium impact medium impact
MutationAssessor transf score 0.47 1.46
CHASM Neutral Neutral
CHASM pvalue 0.57 0.55
CHASM FDR 0.9 0.9
ClinVar id 692602.0 .
ClinVar Allele id 681138.0 .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 .
ClinVar CLNDN Leigh_syndrome .
ClinVar CLNSIG Uncertain_significance .
MITOMAP Disease Clinical info . .
MITOMAP Disease Status . .
MITOMAP Disease Hom/Het ./. ./.
MITOMAP General GenBank Freq 0.0016% .
MITOMAP General GenBank Seqs 1 .
MITOMAP General Curated refs . .
MITOMAP Variant Class polymorphism .
gnomAD 3.1 AN 56434.0 .
gnomAD 3.1 AC Homo 5.0 .
gnomAD 3.1 AF Hom 8.85991e-05 .
gnomAD 3.1 AC Het 0.0 .
gnomAD 3.1 AF Het 0.0 .
gnomAD 3.1 filter PASS .
HelixMTdb AC Hom 2.0 .
HelixMTdb AF Hom 1.0204967e-05 .
HelixMTdb AC Het 0.0 .
HelixMTdb AF Het 0.0 .
HelixMTdb mean ARF . .
HelixMTdb max ARF . .
ToMMo 54KJPN AC 1 .
ToMMo 54KJPN AF 1.8e-05 .
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