Chr |
chrM |
chrM |
chrM |
Start |
9035 |
9035 |
9035 |
End |
9035 |
9035 |
9035 |
Ref |
T |
T |
T |
Alt |
C |
A |
G |
MitImpact id |
MI.1085 |
MI.1083 |
MI.1084 |
Gene symbol |
MT-ATP6 |
MT-ATP6 |
MT-ATP6 |
Respiratory Chain complex |
V |
V |
V |
Ensembl gene id |
ENSG00000198899 |
ENSG00000198899 |
ENSG00000198899 |
Ensembl protein id |
ENSP00000354632 |
ENSP00000354632 |
ENSP00000354632 |
Ensembl transcript id |
ENST00000361899 |
ENST00000361899 |
ENST00000361899 |
Uniprot name |
ATP6_HUMAN |
ATP6_HUMAN |
ATP6_HUMAN |
Uniprot id |
P00846 |
P00846 |
P00846 |
Ncbi gene id |
4508 |
4508 |
4508 |
Ncbi protein id |
YP_003024031.1 |
YP_003024031.1 |
YP_003024031.1 |
Gene position |
509 |
509 |
509 |
AA position |
170 |
170 |
170 |
AA ref |
L |
L |
L |
AA alt |
P |
H |
R |
Codon substitution |
cTc/cCc |
cTc/cAc |
cTc/cGc |
PhyloP 100V |
-1.72 |
-1.72 |
-1.72 |
PhastCons 100V |
0 |
0 |
0 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1 |
1 |
1 |
SIFT |
deleterious |
deleterious |
deleterious |
SIFT score |
0 |
0 |
0 |
FatHmm |
deleterious |
deleterious |
deleterious |
FatHmm score |
-5.85 |
-5.89 |
-5.31 |
FatHmmW |
neutral |
neutral |
neutral |
FatHmmW score |
3.81 |
3.81 |
3.81 |
PROVEAN |
deleterious |
deleterious |
deleterious |
PROVEAN score |
-6.22 |
-6.17 |
-5.29 |
MutationAssessor |
high impact |
high impact |
high impact |
MutationAssessor score |
4.45 |
4.45 |
4.45 |
EFIN SP |
damaging |
damaging |
damaging |
EFIN SP score |
0.28 |
0.47 |
0.37 |
EFIN HD |
damaging |
damaging |
damaging |
EFIN HD score |
0.15 |
0.14 |
0.13 |
CADD |
deleterious |
deleterious |
deleterious |
CADD score |
4.03 |
4.32 |
4.25 |
CADD phred |
23.7 |
24 |
23.9 |
VEST pvalue |
0.17 |
0.16 |
0.16 |
VEST FDR |
0.65 |
0.65 |
0.65 |
PANTHER |
disease |
disease |
disease |
PANTHER score |
0.92 |
0.92 |
0.89 |
PhD-SNP |
disease |
disease |
disease |
PhD-SNP score |
0.82 |
0.82 |
0.88 |
SNAP |
disease |
disease |
disease |
SNAP score |
0.74 |
0.71 |
0.74 |
Meta-SNP |
disease |
disease |
disease |
Meta-SNP score |
0.83 |
0.82 |
0.82 |
Meta-SNP RI |
7 |
6 |
6 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1 |
1 |
1 |
Condel |
neutral |
neutral |
neutral |
Condel score |
0 |
0 |
0 |
COVEC WMV |
deleterious |
deleterious |
deleterious |
COVEC WMV score |
6 |
6 |
6 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.89 |
0.87 |
0.9 |
PolyPhen2 transf |
low impact |
low impact |
low impact |
PolyPhen2 transf score |
-3.6 |
-3.6 |
-3.6 |
SIFT_transf |
low impact |
low impact |
low impact |
SIFT transf score |
-1.4 |
-1.4 |
-1.4 |
MutationAssessor transf |
high impact |
high impact |
high impact |
MutationAssessor transf score |
2.72 |
2.72 |
2.72 |
CHASM pvalue |
0.69 |
0.52 |
0.51 |
CHASM FDR |
0.9 |
0.9 |
0.9 |
APOGEE |
Pathogenic |
Likely-pathogenic |
Pathogenic |
APOGEE score |
0.9774592772708436 |
0.8745249742300166 |
0.946570512202185 |
SNPDryad score |
1 |
0.97 |
0.99 |
MutationTaster |
disease_causing |
polymorphism |
polymorphism |
MutationTaster score |
0.99 |
1 |
1 |
DEOGEN2 score |
0.32 |
0.32 |
0.31 |
Mitoclass.1 |
damaging |
damaging |
damaging |
dbSNP 155 id |
rs1603222000 |
. |
. |
ClinVar October2021 Variation id |
690280 |
. |
. |
ClinVar October2021 CLNSIG |
Likely_pathogenic |
. |
. |
ClinVar October2021 CLNDN |
See_cases|Leber_optic_atrophy|Progressive_cerebellar_ataxia|Leigh_syndrome|Mitochondrial_disease |
. |
. |
ClinVar October2021 CLNDISDB |
.|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:ORPHA104,SNOMED_CT:58610003|Human_Phenotype_Ontology:HP:0001329,Human_Phenotype_Ontology:HP:0002073,Human_Phenotype_Ontology:HP:0002496,Human_Phenotype_Ontology:HP:0007331,MedGen:C0393525|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:ORPHA506,SNOMED_CT:29570005|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:ORPHA68380 |
. |
. |
COSMIC 90 |
. |
. |
. |
MITOMAP Allele |
T9035C |
. |
. |
MITOMAP Disease Het/Hom |
+/+ |
. |
. |
MITOMAP Disease Clinical info |
Ataxia syndromes |
. |
. |
MITOMAP Disease Status |
Cfrm |
. |
. |
MITOMAP Disease GenBank Freq |
0.000% |
. |
. |
MITOMAP Disease GenBank Seqs |
0 (0) |
. |
. |
MITOMAP Disease GenBank Curated refs |
5 |
. |
. |
MITOMAP General GenBank Freq |
. |
. |
. |
MITOMAP General GenBank Seqs |
. |
. |
. |
MITOMAP General Curated refs |
. |
. |
. |
gnomAD 3.1 filter |
PASS |
. |
. |
gnomAD 3.1 AC Homo |
0 |
. |
. |
gnomAD 3.1 AC Het |
2 |
. |
. |
gnomAD 3.1 AF Hom |
0 |
. |
. |
gnomAD 3.1 AF Het |
3.5446537e-05 |
. |
. |
gnomAD 3.1 AN |
56423 |
. |
. |
HelixMTdb AC Hom |
0 |
. |
. |
HelixMTdb AF Hom |
0 |
. |
. |
HelixMTdb AC Het |
8 |
. |
. |
HelixMTdb AF Het |
4.081987e-05 |
. |
. |
HelixMTdb mean ARF |
0.25609 |
. |
. |
HelixMTdb max ARF |
0.5098 |
. |
. |
EVmutation |
MT-ATP6_170L|199L:0.292524;196L:0.189155;221Y:0.156577;206V:0.126652;173L:0.102339;201I:0.090527;200T:0.085895;174I:0.070758;203E:0.064958 |
MT-ATP6_170L|199L:0.292524;196L:0.189155;221Y:0.156577;206V:0.126652;173L:0.102339;201I:0.090527;200T:0.085895;174I:0.070758;203E:0.064958 |
MT-ATP6_170L|199L:0.292524;196L:0.189155;221Y:0.156577;206V:0.126652;173L:0.102339;201I:0.090527;200T:0.085895;174I:0.070758;203E:0.064958 |
Site A InterP |
ATP6_170 |
ATP6_170 |
ATP6_170 |
Site B InterP |
ATP8_51 |
ATP8_51 |
ATP8_51 |
Covariation Score InterP |
mfDCA_34.47 |
mfDCA_34.47 |
mfDCA_34.47 |
Site A IntraP |
. |
. |
. |
Site B IntraP |
. |
. |
. |
Covariation Score IntraP |
. |
. |
. |
CPD AA ref |
. |
. |
. |
CPD AA alt |
. |
. |
. |
CPD Aln pos |
. |
. |
. |
CPD Frequency |
. |
. |
. |
CPD Species name |
. |
. |
. |
CPD RefSeq Protein ID |
. |
. |
. |
CPD Ncbi Taxon id |
. |
. |
. |
DDG intra |
. |
. |
. |
DDG intra interface |
. |
. |
. |
DDG inter |
. |
. |
. |