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
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
350
AA pos
117
AA ref
M
AA alt
T
Codon substitution
aTa/aCa
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Conservation

PhyloP 100v
4.06
PhastCons 100v
0.99

Pathogenicity predictors

PolyPhen2
Benign
PolyPhen2 score
0
SIFT
Neutral
SIFT score
0.37
FatHmm
Neutral
FatHmm score
-0.56
FatHMMW
Neutral
FatHMMW score
2.79
PROVEAN
Neutral
PROVEAN score
-2.08
Mutation Assessor
Medium impact
Mutation Assessor score
2.12
EFIN SP
Neutral
EFIN SP score
0.79
EFIN HD
Neutral
EFIN HD score
0.98
VEST p-value
0.5
VEST FDR
0.55
PANTHER
Neutral
PANTHER score
0.31
PhD-SNP
Neutral
PhD-SNP score
0.36
MutationTaster
Polymorphism
MutationTaster score
1
CADD
Neutral
CADD score
-0.64
CADD phred
0.1
SNAP
Neutral
SNAP score
0.49
MitoClass 1
Neutral
SNPDryad score
0.01

Pathogenicity meta-predictors

CAROL
Neutral
CAROL score
0.63
Condel
Deleterious
Condel score
0.69
COVEC WMV
Neutral
COVEC WMV score
-3
Meta SNP
Neutral
Meta SNP score
0.45
Meta SNP RI
1
MtoolBox
Neutral
MtoolBox DS
0.13
APOGEE
P
APOGEE score
0.67
DEOGEN2 score
0.03

Cancer-specific predictors

PolyPhen2 transf
High impact
PolyPhen2 transf score
2.07
SIFT transf
Medium impact
SIFT transf score
0.06
MutationAssessor transf
Medium impact
MutationAssessor transf score
0.86
CHASM p-value
0.34
CHASM FDR
0.9

Residue interaction

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

Databases of Allelic frequency & Phenotype

ClinVar March2020 ClinSig
Benign
ClinVar March2020 ClnDBN
Leigh syndrome
ClinVar March2020 ClnAllele ID
681167
ClinVar March2020 ClnDSDB
Medgen:c0023264, omim:256000, orphanet:orpha506, snomed ct:29570005
MITOMAP Allele
T6253c
MITOMAP Phenotype
Prostate cancer / enriched in poag cohort
MITOMAP Homoplasmy
+
MITOMAP Heteroplasmy
-
MITOMAP Status
Reported
MITOMAP NRef
3
COSMIC 90
.
dbSNP 153
Rs200165736

Pathogenic variants, CPD

Frequency
14.09
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

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
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
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
4.06
PhastCons 100v
0.99

Pathogenicity predictors

PolyPhen2
Benign
PolyPhen2 score
0.01
SIFT
Neutral
SIFT score
0.16
FatHmm
Neutral
FatHmm score
-2.07
FatHMMW
Neutral
FatHMMW score
2.76
PROVEAN
Deleterious
PROVEAN score
-2.75
Mutation Assessor
Medium impact
Mutation Assessor score
3.24
EFIN SP
Neutral
EFIN SP score
0.66
EFIN HD
Neutral
EFIN HD score
0.41
VEST p-value
0.28
VEST FDR
0.55
PANTHER
Disease
PANTHER score
0.53
PhD-SNP
Disease
PhD-SNP score
0.69
MutationTaster
Polymorphism
MutationTaster score
1
CADD
Neutral
CADD score
0.69
CADD phred
8.75
SNAP
Disease
SNAP score
0.66
MitoClass 1
Damaging
SNPDryad score
0.69

Pathogenicity meta-predictors

CAROL
Neutral
CAROL score
0.84
Condel
Deleterious
Condel score
0.58
COVEC WMV
Neutral
COVEC WMV score
-3
Meta SNP
Disease
Meta SNP score
0.71
Meta SNP RI
4
MtoolBox
Neutral
MtoolBox DS
0.23
APOGEE
P
APOGEE score
0.53
DEOGEN2 score
0.1

Cancer-specific predictors

PolyPhen2 transf
Medium impact
PolyPhen2 transf score
1.12
SIFT transf
Medium impact
SIFT transf score
-0.21
MutationAssessor transf
Medium impact
MutationAssessor transf score
1.89
CHASM p-value
0.64
CHASM FDR
0.9

Residue interaction

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

Databases of Allelic frequency & Phenotype

ClinVar March2020 ClinSig
.
ClinVar March2020 ClnDBN
.
ClinVar March2020 ClnAllele ID
.
ClinVar March2020 ClnDSDB
.
MITOMAP Allele
.
MITOMAP Phenotype
.
MITOMAP Homoplasmy
.
MITOMAP Heteroplasmy
.
MITOMAP Status
.
MITOMAP NRef
.
COSMIC 90
.
dbSNP 153
.

Pathogenic variants, CPD

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.
~ 6253 (T/C) 6253 (T/A)
~ 6253 (aTa/aCa) 6253 (aTa/aAa)
Chr chrM chrM
Start 6253 6253
End 6253 6253
Ref T T
Alt C A
MitImpact id MI.2629 MI.2630
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 T K
Codon substitution aTa/aCa aTa/aAa
PhyloP 100V 4.06 4.06
PhastCons 100V 0.99 0.99
PolyPhen2 benign benign
PolyPhen2 score 0 0.01
SIFT neutral neutral
SIFT score 0.37 0.16
FatHmm neutral neutral
FatHmm score -0.56 -2.07
FatHmmW neutral neutral
FatHmmW score 2.79 2.76
PROVEAN neutral deleterious
PROVEAN score -2.08 -2.75
MutationAssessor medium impact medium impact
MutationAssessor score 2.12 3.24
EFIN SP neutral neutral
EFIN SP score 0.79 0.66
EFIN HD neutral neutral
EFIN HD score 0.98 0.41
CADD neutral neutral
CADD score -0.64 0.69
CADD phred 0.1 8.75
VEST pvalue 0.5 0.28
VEST FDR 0.55 0.55
PANTHER neutral disease
PANTHER score 0.31 0.53
PhD-SNP neutral disease
PhD-SNP score 0.36 0.69
SNAP neutral disease
SNAP score 0.49 0.66
Meta-SNP neutral disease
Meta-SNP score 0.45 0.71
Meta-SNP RI 1 4
CAROL neutral neutral
CAROL score 0.63 0.84
Condel deleterious deleterious
Condel score 0.69 0.58
COVEC WMV neutral neutral
COVEC WMV score -3 -3
MtoolBox neutral neutral
MtoolBox DS 0.13 0.23
PolyPhen2 transf high impact medium impact
PolyPhen2 transf score 2.07 1.12
SIFT_transf medium impact medium impact
SIFT transf score 0.06 -0.21
MutationAssessor transf medium impact medium impact
MutationAssessor transf score 0.86 1.89
CHASM pvalue 0.34 0.64
CHASM FDR 0.9 0.9
APOGEE P P
APOGEE score 0.67 0.53
SNPDryad score 0.01 0.69
MutationTaster polymorphism polymorphism
MutationTaster score 1 1
DEOGEN2 score 0.03 0.1
Mitoclass.1 neutral damaging
dbSNP 153 id rs200165736 .
ClinVar March2020 ClinSig Benign .
ClinVar March2020 ClnDBN Leigh_syndrome .
ClinVar March2020 ClnAllele id 681167 .
ClinVar March2020 ClnDSDB MedGen:C0023264,OMIM:256000,Orphanet:ORPHA506,SNOMED_CT:29570005 .
COSMIC 90 . .
CPD Frequency 14.09 .
MITOMAP Allele T6253C .
MITOMAP Phenotype Prostate Cancer / enriched in POAG cohort .
MITOMAP Homoplasmy + .
MITOMAP Heteroplasmy - .
MITOMAP Status Reported .
MITOMAP NRef 3 .
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:51.0897;cMI:219.650101;cMI:182.408829;cMI:148.307785;cMI:140.301331;cMI:136.627319 mfDCA:45.88;mfDCA:51.0897;cMI:219.650101;cMI:182.408829;cMI:148.307785;cMI:140.301331;cMI:136.627319
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 Species name . .
CPD RefSeq Protein ID . .
CPD Ncbi Taxon id . .
DDG intra 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 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
DDG intra interface . .
DDG inter . .
For more info, please check the output legend.
For more info, please check the output legend.
For more info, please check the output legend.
For more info, please check the output legend.
For more info, please check the output legend.