Chr |
chrM |
chrM |
Start |
8851 |
8851 |
End |
8851 |
8851 |
Ref |
T |
T |
Alt |
C |
G |
MitImpact id |
MI.689 |
MI.690 |
Gene symbol |
MT-ATP6 |
MT-ATP6 |
Respiratory Chain complex |
V |
V |
Ensembl gene id |
ENSG00000198899 |
ENSG00000198899 |
Ensembl protein id |
ENSP00000354632 |
ENSP00000354632 |
Ensembl transcript id |
ENST00000361899 |
ENST00000361899 |
Uniprot name |
ATP6_HUMAN |
ATP6_HUMAN |
Uniprot id |
P00846 |
P00846 |
Ncbi gene id |
4508 |
4508 |
Ncbi protein id |
YP_003024031.1 |
YP_003024031.1 |
Gene position |
325 |
325 |
AA position |
109 |
109 |
AA ref |
W |
W |
AA alt |
R |
G |
Codon substitution |
Tga/Cga |
Tga/Gga |
PhyloP 100V |
-6.58 |
-6.58 |
PhastCons 100V |
0 |
0 |
PolyPhen2 |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1 |
0.99 |
SIFT |
deleterious |
deleterious |
SIFT score |
0 |
0 |
FatHmm |
deleterious |
neutral |
FatHmm score |
-3.07 |
-2.76 |
FatHmmW |
neutral |
neutral |
FatHmmW score |
4.18 |
4.15 |
PROVEAN |
deleterious |
deleterious |
PROVEAN score |
-12.91 |
-11.98 |
MutationAssessor |
high impact |
high impact |
MutationAssessor score |
4.46 |
4.46 |
EFIN SP |
damaging |
neutral |
EFIN SP score |
0.41 |
0.62 |
EFIN HD |
damaging |
neutral |
EFIN HD score |
0.25 |
0.42 |
CADD |
deleterious |
deleterious |
CADD score |
3.56 |
3.87 |
CADD phred |
23.1 |
23.5 |
VEST pvalue |
0.28 |
0.24 |
VEST FDR |
0.65 |
0.65 |
PANTHER |
disease |
disease |
PANTHER score |
0.82 |
0.83 |
PhD-SNP |
disease |
disease |
PhD-SNP score |
0.96 |
0.92 |
SNAP |
disease |
disease |
SNAP score |
0.79 |
0.75 |
Meta-SNP |
disease |
disease |
Meta-SNP score |
0.77 |
0.71 |
Meta-SNP RI |
5 |
4 |
CAROL |
deleterious |
deleterious |
CAROL score |
1 |
1 |
Condel |
neutral |
neutral |
Condel score |
0 |
0.01 |
COVEC WMV |
deleterious |
deleterious |
COVEC WMV score |
6 |
6 |
MtoolBox |
deleterious |
deleterious |
MtoolBox DS |
0.9 |
0.84 |
PolyPhen2 transf |
low impact |
low impact |
PolyPhen2 transf score |
-3.6 |
-2.65 |
SIFT_transf |
low impact |
low impact |
SIFT transf score |
-1.4 |
-1.4 |
MutationAssessor transf |
high impact |
high impact |
MutationAssessor transf score |
2.72 |
2.72 |
CHASM pvalue |
0.24 |
0.28 |
CHASM FDR |
0.9 |
0.9 |
APOGEE |
Likely-pathogenic |
Likely-pathogenic |
APOGEE score |
0.8674358909547452 |
0.7289547133207903 |
SNPDryad score |
0.97 |
1 |
MutationTaster |
disease_causing_automatic |
disease_causing |
MutationTaster score |
0.98 |
0.99 |
DEOGEN2 score |
0.43 |
0.41 |
Mitoclass.1 |
damaging |
damaging |
dbSNP 155 id |
rs199476136 |
. |
ClinVar October2021 Variation id |
9645 |
. |
ClinVar October2021 CLNSIG |
Uncertain_significance |
. |
ClinVar October2021 CLNDN |
Leber_optic_atrophy|Leigh_syndrome|Striatonigral_degeneration,_infantile,_mitochondrial|Mitochondrial_disease|not_provided |
. |
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|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:ORPHA506,SNOMED_CT:29570005|MONDO:MONDO:0010774,MedGen:C1839022,OMIM:500003|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:ORPHA68380|MedGen:CN517202 |
. |
COSMIC 90 |
. |
. |
MITOMAP Allele |
T8851C |
. |
MITOMAP Disease Het/Hom |
+/+ |
. |
MITOMAP Disease Clinical info |
BSN / Leigh syndrome |
. |
MITOMAP Disease Status |
Cfrm [VUS*] |
. |
MITOMAP Disease GenBank Freq |
0.000% |
. |
MITOMAP Disease GenBank Seqs |
3 (0) |
. |
MITOMAP Disease GenBank Curated refs |
9 |
. |
MITOMAP General GenBank Freq |
. |
. |
MITOMAP General GenBank Seqs |
. |
. |
MITOMAP General Curated refs |
. |
. |
gnomAD 3.1 filter |
PASS |
npg |
gnomAD 3.1 AC Homo |
2 |
0 |
gnomAD 3.1 AC Het |
0 |
0 |
gnomAD 3.1 AF Hom |
3.5443398e-05 |
0 |
gnomAD 3.1 AF Het |
0 |
0 |
gnomAD 3.1 AN |
56428 |
56433 |
HelixMTdb AC Hom |
10 |
. |
HelixMTdb AF Hom |
5.102484e-05 |
. |
HelixMTdb AC Het |
4 |
. |
HelixMTdb AF Het |
2.040993e-05 |
. |
HelixMTdb mean ARF |
0.29899 |
. |
HelixMTdb max ARF |
0.59701 |
. |
EVmutation |
MT-ATP6_109W|153P:0.295096;112T:0.25175;110A:0.229063;156L:0.197917;148S:0.176581;113V:0.162301;149L:0.156156;152Q:0.136676;221Y:0.131585;114I:0.111246;151I:0.094802;129L:0.093224;173L:0.092062;223H:0.089033;165T:0.084286;145E:0.075977;158V:0.07021;150L:0.069853;163N:0.065282;207A:0.063482 |
MT-ATP6_109W|153P:0.295096;112T:0.25175;110A:0.229063;156L:0.197917;148S:0.176581;113V:0.162301;149L:0.156156;152Q:0.136676;221Y:0.131585;114I:0.111246;151I:0.094802;129L:0.093224;173L:0.092062;223H:0.089033;165T:0.084286;145E:0.075977;158V:0.07021;150L:0.069853;163N:0.065282;207A:0.063482 |
Site A InterP |
. |
. |
Site B InterP |
. |
. |
Covariation Score InterP |
. |
. |
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 |
. |
. |