Chr |
chrM |
chrM |
chrM |
Start |
9176 |
9176 |
9176 |
End |
9176 |
9176 |
9176 |
Ref |
T |
T |
T |
Alt |
G |
C |
A |
MitImpact id |
MI.1385 |
MI.1384 |
MI.1383 |
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 |
650 |
650 |
650 |
AA position |
217 |
217 |
217 |
AA ref |
L |
L |
L |
AA alt |
R |
P |
Q |
Codon substitution |
cTa/cGa |
cTa/cCa |
cTa/cAa |
PhyloP 100V |
5.87961 |
5.87961 |
5.87961 |
PhastCons 100V |
0.905512 |
0.905512 |
0.905512 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1.0 |
1.0 |
1.0 |
SIFT |
deleterious |
deleterious |
deleterious |
SIFT score |
0 |
0 |
0 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0 |
0 |
0 |
FatHmm |
deleterious |
deleterious |
deleterious |
FatHmm score |
-9.28 |
-9.53 |
-9.42 |
FatHmmW |
neutral |
neutral |
neutral |
FatHmmW score |
2.16 |
2.16 |
2.16 |
PROVEAN |
deleterious |
deleterious |
deleterious |
PROVEAN score |
-5.36 |
-6.26 |
-5.35 |
MutationAssessor |
high impact |
high impact |
high impact |
MutationAssessor score |
4.57 |
4.22 |
4.57 |
EFIN SP |
damaging |
damaging |
damaging |
EFIN SP score |
0.18 |
0.06 |
0.41 |
EFIN HD |
neutral |
neutral |
neutral |
EFIN HD score |
0.36 |
0.44 |
0.45 |
CADD |
deleterious |
deleterious |
deleterious |
CADD score |
4.29 |
4 |
4.13 |
CADD phred |
24 |
23.6 |
23.8 |
VEST pvalue |
0.11 |
0.12 |
0.11 |
VEST FDR |
0.65 |
0.65 |
0.65 |
PANTHER |
. |
. |
. |
PANTHER score |
. |
. |
. |
PhD-SNP |
disease |
disease |
disease |
PhD-SNP score |
0.88 |
0.8 |
0.82 |
SNAP |
disease |
disease |
disease |
SNAP score |
0.85 |
0.84 |
0.79 |
Meta-SNP |
disease |
disease |
disease |
Meta-SNP score |
0.84 |
0.78 |
0.76 |
Meta-SNP RI |
7 |
6 |
5 |
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 |
0.92 |
0.92 |
0.87 |
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 |
2.82 |
2.52 |
2.82 |
CHASM pvalue |
0.37 |
0.54 |
0.61 |
CHASM FDR |
0.9 |
0.9 |
0.9 |
APOGEE1 |
Pathogenic |
Pathogenic |
Pathogenic |
APOGEE1 score |
0.9 |
0.92 |
0.66 |
APOGEE2 |
Pathogenic |
Pathogenic |
Likely-pathogenic |
APOGEE2 score |
0.957153322162873 |
0.969106537719339 |
0.901111889759993 |
SNPDryad score |
0.99 |
1 |
0.98 |
MutationTaster |
disease_causing_automatic |
disease_causing_automatic |
disease_causing |
MutationTaster score |
0.9 |
1 |
0.88 |
DEOGEN2 score |
0.41 |
0.42 |
0.41 |
Mitoclass.1 |
damaging |
damaging |
damaging |
dbSNP 155 id |
rs199476135 |
rs199476135 |
. |
ClinVar July2022 Variation id |
9650 |
9644 |
. |
ClinVar July2022 CLNSIG |
Likely_pathogenic |
Pathogenic |
. |
ClinVar July2022 CLNDN |
Leber_optic_atrophy|Leigh_syndrome|Mitochondrial_complex_5_(ATP_synthase)_deficiency,_mitochondrial_type_1|Mitochondrial_disease|not_provided |
Leber_optic_atrophy|Leigh_syndrome|Striatonigral_degeneration,_infantile,_mitochondrial|Maternally-inherited_spastic_paraplegia|Mitochondrial_complex_5_(ATP_synthase)_deficiency,_mitochondrial_type_1|Mitochondrial_disease|not_provided |
. |
ClinVar July2022 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:0027069,MedGen:C3275684,OMIM:500015|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:ORPHA68380|MedGen:CN517202 |
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:0017917,MedGen:C4755299,Orphanet:ORPHA320360|MONDO:MONDO:0027069,MedGen:C3275684,OMIM:500015|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:ORPHA68380|MedGen:CN517202 |
. |
COSMIC 90 |
. |
. |
. |
MITOMAP Allele |
T9176G |
T9176C |
. |
MITOMAP Disease Het/Hom |
+/+ |
+/+ |
. |
MITOMAP Disease Clinical info |
Leigh Disease / Spastic Paraplegia / Spinocerebellar Ataxia |
FBSN / Leigh Disease / Spinocerebellar Ataxia |
. |
MITOMAP Disease Status |
Cfrm [LP] |
Cfrm [P] |
. |
MITOMAP Disease GenBank Freq |
0.002%(0.000%) |
0.005%(0.000%) |
. |
MITOMAP Disease GenBank Seqs |
1 (0) |
3 (0) |
. |
MITOMAP Disease GenBank Curated refs |
11 |
35 |
. |
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 |
. |
3 |
. |
gnomAD 3.1 AF Hom |
. |
0 |
. |
gnomAD 3.1 AF Het |
. |
0.000053160384 |
. |
gnomAD 3.1 AN |
. |
56433 |
. |
HelixMTdb AC Hom |
. |
1.0 |
. |
HelixMTdb AF Hom |
. |
5.1024836e-06 |
. |
HelixMTdb AC Het |
. |
0.0 |
. |
HelixMTdb AF Het |
. |
0.0 |
. |
HelixMTdb mean ARF |
. |
. |
. |
HelixMTdb max ARF |
. |
. |
. |
EVmutation |
MT-ATP6_217L|221Y:0.106331 |
MT-ATP6_217L|221Y:0.106331 |
MT-ATP6_217L|221Y:0.106331 |
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 |
. |
. |
. |