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6253 (T > A)

General info

Chr
chrM
Start
6253
End
6253
Ref
T
Alt
A
Mitimpact ID
MI.2630
Gene symbol
MT-CO1
RC complex
IV
Ensembl gene ID
ENSG00000198804
Ensembl protein ID
ENSP00000354499
Ensembl transcript ID
ENST00000361624
Uniprot name
COX1_HUMAN
Uniprot ID
P00395
Ncbi gene ID
4512
Ncbi protein ID
YP_003024028.1
Gene position
350
AA pos
117
AA ref
M
AA alt
K
Codon substitution
aTa/aAa
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Powered by MitoWheel

Conservation

PhyloP 100v
1.93161 Conservation Score
PhastCons 100v
0.968504 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
FatHmm
Neutral Score and details of the predictor
FatHMMW
Neutral Score and details of the predictor
PROVEAN
Deleterious Score and details of the predictor
Mutation Assessor
Medium impact Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
CADD
Neutral Score and details of the predictor
SNAP
Disease Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Vus- 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
Meta SNP
Disease Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Neutral Score and details of the meta-predictor

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 Phenotypes

ClinVar July2022 CLNSIG
.
ClinVar July2022 CLNDN
.
ClinVar July2022 Variation ID
.
ClinVar July2022 CLNDISDB
.
MITOMAP Allele
.
MITOMAP Disease Het/Hom
.
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease GenBank Freq
.
MITOMAP Disease GenBank Seqs
.
MITOMAP Disease GenBank Curated refs
.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
Gnomad31 filter
.
Gnomad31 AC hom
.
Gnomad31 AC het
.
Gnomad31 AF hom
.
Gnomad31 AF het
.
Gnomad31 AN
.
HelixMTdb AC hom
.
HelixMTdb AF hom
.
HelixMTdb AC het
.
HelixMTdb AF het
.
HelixMTdb mean ARF
.
HelixMTdb max ARF
.
COSMIC 90
.
dbSNP 155
.

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
.

6253 (T > C)

General info

Chr
chrM
Start
6253
End
6253
Ref
T
Alt
C
Mitimpact ID
MI.2629
Gene symbol
MT-CO1
RC complex
IV
Ensembl gene ID
ENSG00000198804
Ensembl protein ID
ENSP00000354499
Ensembl transcript ID
ENST00000361624
Uniprot name
COX1_HUMAN
Uniprot ID
P00395
Ncbi gene ID
4512
Ncbi protein ID
YP_003024028.1
Gene position
350
AA pos
117
AA ref
M
AA alt
T
Codon substitution
aTa/aCa
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
1.93161 Conservation Score
PhastCons 100v
0.968504 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
FatHmm
Neutral Score and details of the predictor
FatHMMW
Neutral Score and details of the predictor
PROVEAN
Neutral Score and details of the predictor
Mutation Assessor
Medium impact Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
Neutral Score and details of the predictor
PhD-SNP
Neutral Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
CADD
Neutral Score and details of the predictor
SNAP
Neutral Score and details of the predictor
MitoClass 1
Neutral Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor

Pathogenicity meta-predictors

APOGEE1
Pathogenic 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
Meta SNP
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Neutral Score and details of the meta-predictor

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
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar July2022 CLNSIG
.
ClinVar July2022 CLNDN
.
ClinVar July2022 Variation ID
.
ClinVar July2022 CLNDISDB
.
MITOMAP Allele
6253T>C
MITOMAP Disease Het/Hom
+/-
MITOMAP Disease Clinical info
Prostate cancer / enriched in poag cohort
MITOMAP Disease Status
Reported
MITOMAP Disease GenBank Freq
0.990%(0.000%)
MITOMAP Disease GenBank Seqs
588 (0)
MITOMAP Disease GenBank Curated refs
3
MITOMAP General GenBank Freq
0.0099
MITOMAP General GenBank Seqs
588
MITOMAP General GenBank Curated refs
12
Gnomad31 filter
Pass
Gnomad31 AC hom
656
Gnomad31 AC het
1
Gnomad31 AF hom
0.01162564
Gnomad31 AF het
0.000017722012
Gnomad31 AN
56427
HelixMTdb AC hom
997.0
HelixMTdb AF hom
0.005087176
HelixMTdb AC het
7.0
HelixMTdb AF het
3.5717385e-05
HelixMTdb mean ARF
0.28737
HelixMTdb max ARF
0.66426
COSMIC 90
.
dbSNP 155
rs200165736

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
14.09 CPD variant frequency
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.
~ 6253 (T/A) 6253 (T/C)
~ 6253 (aTa/aAa) 6253 (aTa/aCa)
Chr chrM chrM
Start 6253 6253
End 6253 6253
Ref T T
Alt A C
MitImpact id MI.2630 MI.2629
Gene symbol MT-CO1 MT-CO1
Respiratory Chain complex IV IV
Ensembl gene id ENSG00000198804 ENSG00000198804
Ensembl protein id ENSP00000354499 ENSP00000354499
Ensembl transcript id ENST00000361624 ENST00000361624
Uniprot name COX1_HUMAN COX1_HUMAN
Uniprot id P00395 P00395
Ncbi gene id 4512 4512
Ncbi protein id YP_003024028.1 YP_003024028.1
Gene position 350 350
AA position 117 117
AA ref M M
AA alt K T
Codon substitution aTa/aAa aTa/aCa
PhyloP 100V 1.93161 1.93161
PhastCons 100V 0.968504 0.968504
PolyPhen2 benign benign
PolyPhen2 score 0.01 0.0
SIFT neutral neutral
SIFT score 0.16 0.37
SIFT4G Tolerated Tolerated
SIFT4G score 0.063 0.321
FatHmm neutral neutral
FatHmm score -2.07 -0.56
FatHmmW neutral neutral
FatHmmW score 2.76 2.79
PROVEAN deleterious neutral
PROVEAN score -2.75 -2.08
MutationAssessor medium impact medium impact
MutationAssessor score 3.24 2.12
EFIN SP neutral neutral
EFIN SP score 0.66 0.79
EFIN HD neutral neutral
EFIN HD score 0.41 0.98
CADD neutral neutral
CADD score 0.69 -0.64
CADD phred 8.75 0.1
VEST pvalue 0.28 0.5
VEST FDR 0.55 0.55
PANTHER disease neutral
PANTHER score 0.53 0.31
PhD-SNP disease neutral
PhD-SNP score 0.69 0.36
SNAP disease neutral
SNAP score 0.66 0.49
Meta-SNP disease neutral
Meta-SNP score 0.71 0.45
Meta-SNP RI 4 1
CAROL neutral neutral
CAROL score 0.84 0.63
Condel deleterious deleterious
Condel score 0.58 0.69
COVEC WMV neutral neutral
COVEC WMV score -3 -3
MtoolBox neutral neutral
MtoolBox DS 0.23 0.13
PolyPhen2 transf medium impact high impact
PolyPhen2 transf score 1.12 2.07
SIFT_transf medium impact medium impact
SIFT transf score -0.21 0.06
MutationAssessor transf medium impact medium impact
MutationAssessor transf score 1.89 0.86
CHASM pvalue 0.64 0.34
CHASM FDR 0.9 0.9
APOGEE1 Pathogenic Pathogenic
APOGEE1 score 0.53 0.67
APOGEE2 VUS- Benign
APOGEE2 score 0.302163785176961 0.0529658508394979
SNPDryad score 0.69 0.01
MutationTaster polymorphism polymorphism
MutationTaster score 1 1
DEOGEN2 score 0.1 0.03
Mitoclass.1 damaging neutral
dbSNP 155 id . rs200165736
ClinVar July2022 Variation id . .
ClinVar July2022 CLNSIG . .
ClinVar July2022 CLNDN . .
ClinVar July2022 CLNDISDB . .
COSMIC 90 . .
MITOMAP Allele . T6253C
MITOMAP Disease Het/Hom . +/-
MITOMAP Disease Clinical info . Prostate Cancer / enriched in POAG cohort
MITOMAP Disease Status . Reported
MITOMAP Disease GenBank Freq . 0.990%(0.000%)
MITOMAP Disease GenBank Seqs . 588 (0)
MITOMAP Disease GenBank Curated refs . 3
MITOMAP General GenBank Freq . 0.0099
MITOMAP General GenBank Seqs . 588
MITOMAP General Curated refs . 12
gnomAD 3.1 filter . PASS
gnomAD 3.1 AC Homo . 656
gnomAD 3.1 AC Het . 1
gnomAD 3.1 AF Hom . 0.01162564
gnomAD 3.1 AF Het . 0.000017722012
gnomAD 3.1 AN . 56427
HelixMTdb AC Hom . 997.0
HelixMTdb AF Hom . 0.005087176
HelixMTdb AC Het . 7.0
HelixMTdb AF Het . 3.5717385e-05
HelixMTdb mean ARF . 0.28737
HelixMTdb max ARF . 0.66426
EVmutation . .
Site A InterP CO1_117 CO1_117
Site B InterP CO2_86;CO3_60;CO2_99;CO3_50;CO3_179;CO3_49;CO3_27 CO2_86;CO3_60;CO2_99;CO3_50;CO3_179;CO3_49;CO3_27
Covariation Score InterP mfDCA_45.88;mfDCA_51.09;cMI_219.6501;cMI_182.4088;cMI_148.3078;cMI_140.3013;cMI_136.6273 mfDCA_45.88;mfDCA_51.09;cMI_219.6501;cMI_182.4088;cMI_148.3078;cMI_140.3013;cMI_136.6273
Site A IntraP CO1_117 CO1_117
Site B IntraP CO1_146;CO1_466;CO1_487;CO1_415 CO1_146;CO1_466;CO1_487;CO1_415
Covariation Score IntraP cMI_16.38525;mfDCA_26.3292;mfDCA_19.5539;mfDCA_17.6913 cMI_16.38525;mfDCA_26.3292;mfDCA_19.5539;mfDCA_17.6913
CPD AA ref . .
CPD AA alt . .
CPD Aln pos . .
CPD Frequency . 14.09
CPD Species name . .
CPD RefSeq Protein ID . .
CPD Ncbi Taxon id . .
DDG intra MT-CO1:M117K:T415A:-0.697613:-0.55555:-0.0820799;MT-CO1:M117K:T415S:-0.682664:-0.55555:-0.0634344;MT-CO1:M117K:T415I:-1.48679:-0.55555:-0.826481;MT-CO1:M117K:T415P:2.84943:-0.55555:3.35363;MT-CO1:M117K:T415N:-0.823846:-0.55555:-0.192847;MT-CO1:M117K:M466L:-0.0518976:-0.55555:0.623379;MT-CO1:M117K:M466K:0.411581:-0.55555:1.04869;MT-CO1:M117K:M466I:0.233232:-0.55555:0.897034;MT-CO1:M117K:M466V:1.01906:-0.55555:1.64146;MT-CO1:M117K:M466T:0.623853:-0.55555:1.26183 MT-CO1:M117T:T415N:-0.205654:-0.0367906:-0.192847;MT-CO1:M117T:T415P:3.34764:-0.0367906:3.35363;MT-CO1:M117T:T415S:-0.0990778:-0.0367906:-0.0634344;MT-CO1:M117T:T415I:-0.857516:-0.0367906:-0.826481;MT-CO1:M117T:T415A:-0.113605:-0.0367906:-0.0820799;MT-CO1:M117T:M466K:1.06031:-0.0367906:1.04869;MT-CO1:M117T:M466V:1.60224:-0.0367906:1.64146;MT-CO1:M117T:M466T:1.22515:-0.0367906:1.26183;MT-CO1:M117T:M466I:0.865826:-0.0367906:0.897034;MT-CO1:M117T:M466L:0.586175:-0.0367906:0.623379
DDG intra interface . .
DDG inter . .
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.
Score:  
0
  [min -20, max 10]
  • 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]
  • 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 -15, max 10]
  • Neutral:  score > -3
  • Deleterious:  score <= -3
Score:  
0
  [min -3, max 6]
  • Neutral:  score > -1.5
  • Deleterious:  score <= -1.5
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 35]
  • Neutral:  score < 20 (soft threshold)
  • Deleterious:  score >= 20
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]
  • 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