Chr |
chrM |
chrM |
chrM |
Start |
9185 |
9185 |
9185 |
End |
9185 |
9185 |
9185 |
Ref |
T |
T |
T |
Alt |
C |
G |
A |
MitImpact id |
MI.1401 |
MI.1402 |
MI.1403 |
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 |
659 |
659 |
659 |
AA position |
220 |
220 |
220 |
AA ref |
L |
L |
L |
AA alt |
P |
R |
H |
Codon substitution |
cTc/cCc |
cTc/cGc |
cTc/cAc |
PhyloP 100V |
0.82 |
0.82 |
0.82 |
PhastCons 100V |
0.48 |
0.48 |
0.48 |
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 |
-4.18 |
-3.54 |
-4.12 |
FatHmmW |
neutral |
neutral |
neutral |
FatHmmW score |
4.08 |
4.09 |
4.08 |
PROVEAN |
deleterious |
deleterious |
deleterious |
PROVEAN score |
-6.22 |
-5.32 |
-6.2 |
MutationAssessor |
high impact |
high impact |
high impact |
MutationAssessor score |
4.3 |
4.3 |
4.3 |
EFIN SP |
damaging |
damaging |
damaging |
EFIN SP score |
0.2 |
0.15 |
0.38 |
EFIN HD |
neutral |
neutral |
neutral |
EFIN HD score |
0.42 |
0.34 |
0.38 |
CADD |
deleterious |
deleterious |
deleterious |
CADD score |
3.99 |
4.32 |
4.22 |
CADD phred |
23.6 |
24 |
23.9 |
VEST pvalue |
0.2 |
0.19 |
0.22 |
VEST FDR |
0.65 |
0.65 |
0.65 |
PANTHER |
. |
. |
. |
PANTHER score |
. |
. |
. |
PhD-SNP |
disease |
disease |
disease |
PhD-SNP score |
0.67 |
0.78 |
0.7 |
SNAP |
disease |
disease |
disease |
SNAP score |
0.76 |
0.77 |
0.73 |
Meta-SNP |
disease |
disease |
disease |
Meta-SNP score |
0.74 |
0.75 |
0.73 |
Meta-SNP RI |
5 |
5 |
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 |
0.89 |
0.9 |
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 |
2.59 |
2.59 |
2.59 |
CHASM pvalue |
0.48 |
0.54 |
0.58 |
CHASM FDR |
0.9 |
0.9 |
0.9 |
APOGEE |
Likely-pathogenic |
VUS |
Likely-pathogenic |
APOGEE score |
0.9045656434189292 |
0.5696993608763841 |
0.810281980867029 |
SNPDryad score |
1 |
0.99 |
0.97 |
MutationTaster |
disease_causing_automatic |
disease_causing |
disease_causing |
MutationTaster score |
1 |
1 |
1 |
DEOGEN2 score |
0.32 |
0.31 |
0.32 |
Mitoclass.1 |
damaging |
damaging |
damaging |
dbSNP 155 id |
rs199476138 |
rs199476138 |
. |
ClinVar October2021 Variation id |
9647 |
. |
. |
ClinVar October2021 CLNSIG |
Pathogenic |
. |
. |
ClinVar October2021 CLNDN |
Leber_optic_atrophy|Leigh_syndrome|Charcot-Marie-Tooth_disease|Mitochondrial_complex_5_(ATP_synthase)_deficiency,_mitochondrial_type_1|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:0015626,MedGen:C0007959,OMIM:PS118220,Orphanet:ORPHA166,SNOMED_CT:50548001|MONDO:MONDO:0027069,MedGen:C3275684,OMIM:500015|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:ORPHA68380|MedGen:CN517202 |
. |
. |
COSMIC 90 |
. |
. |
. |
MITOMAP Allele |
T9185C |
. |
. |
MITOMAP Disease Het/Hom |
+/+ |
. |
. |
MITOMAP Disease Clinical info |
Leigh Disease / Ataxia syndromes / NARP-like disease / Episodic weakness and Charcot-Marie-Tooth |
. |
. |
MITOMAP Disease Status |
Cfrm |
. |
. |
MITOMAP Disease GenBank Freq |
0.000% |
. |
. |
MITOMAP Disease GenBank Seqs |
3 (0) |
. |
. |
MITOMAP Disease GenBank Curated refs |
34 |
. |
. |
MITOMAP General GenBank Freq |
. |
0.011% |
0.002% |
MITOMAP General GenBank Seqs |
. |
6 |
1 |
MITOMAP General Curated refs |
. |
1 |
1 |
gnomAD 3.1 filter |
PASS |
PASS |
. |
gnomAD 3.1 AC Homo |
0 |
2 |
. |
gnomAD 3.1 AC Het |
2 |
1 |
. |
gnomAD 3.1 AF Hom |
0 |
3.5441513e-05 |
. |
gnomAD 3.1 AF Het |
3.5447792e-05 |
1.7720757e-05 |
. |
gnomAD 3.1 AN |
56421 |
56431 |
. |
HelixMTdb AC Hom |
0 |
15 |
. |
HelixMTdb AF Hom |
0 |
7.653725e-05 |
. |
HelixMTdb AC Het |
2 |
3 |
. |
HelixMTdb AF Het |
1.0204967e-05 |
1.530745e-05 |
. |
HelixMTdb mean ARF |
0.43429 |
0.36981 |
. |
HelixMTdb max ARF |
0.45192 |
0.85025 |
. |
EVmutation |
MT-ATP6_220L|221Y:0.112703;222L:0.073089 |
MT-ATP6_220L|221Y:0.112703;222L:0.073089 |
MT-ATP6_220L|221Y:0.112703;222L:0.073089 |
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 |
. |
. |
. |