~ | 8993 (T/C) | 8993 (T/G) | 8993 (T/A) |
---|---|---|---|
~ | 8993 (cTg/cCg) | 8993 (cTg/cGg) | 8993 (cTg/cAg) |
Chr | chrM | chrM | chrM |
Start | 8993 | 8993 | 8993 |
End | 8993 | 8993 | 8993 |
Ref | T | T | T |
Alt | C | G | A |
MitImpact id | MI.997 | MI.995 | MI.996 |
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 | 467 | 467 | 467 |
AA position | 156 | 156 | 156 |
AA ref | L | L | L |
AA alt | P | R | Q |
Codon substitution | cTg/cCg | cTg/cGg | cTg/cAg |
PhyloP 100V | 5.87961 | 5.87961 | 5.87961 |
PhastCons 100V | 0.897638 | 0.897638 | 0.897638 |
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 | 0.007 | 0 |
FatHmm | deleterious | deleterious | deleterious |
FatHmm score | -8.95 | -8.72 | -8.91 |
FatHmmW | neutral | neutral | neutral |
FatHmmW score | 2.25 | 2.25 | 2.25 |
PROVEAN | deleterious | deleterious | deleterious |
PROVEAN score | -5.96 | -5.18 | -5.16 |
MutationAssessor | high impact | high impact | high impact |
MutationAssessor score | 4.63 | 4.63 | 4.63 |
EFIN SP | damaging | damaging | damaging |
EFIN SP score | 0.05 | 0.06 | 0.36 |
EFIN HD | neutral | neutral | neutral |
EFIN HD score | 0.51 | 0.42 | 0.48 |
CADD | deleterious | deleterious | deleterious |
CADD score | 3.98 | 4.27 | 4.27 |
CADD phred | 23.6 | 24 | 24 |
VEST pvalue | 0.12 | 0.1 | 0.12 |
VEST FDR | 0.65 | 0.65 | 0.65 |
PANTHER | disease | disease | disease |
PANTHER score | 0.93 | 0.88 | 0.89 |
PhD-SNP | disease | disease | disease |
PhD-SNP score | 0.83 | 0.88 | 0.83 |
SNAP | disease | disease | disease |
SNAP score | 0.83 | 0.84 | 0.76 |
Meta-SNP | disease | disease | disease |
Meta-SNP score | 0.87 | 0.87 | 0.82 |
Meta-SNP RI | 7 | 7 | 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 | 0.9 | 0.91 | 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 | 2.87 | 2.87 | 2.87 |
CHASM pvalue | 0.43 | 0.48 | 0.68 |
CHASM FDR | 0.9 | 0.9 | 0.9 |
APOGEE1 | Pathogenic | Pathogenic | Pathogenic |
APOGEE1 score | 0.95 | 0.95 | 0.7 |
APOGEE2 | Pathogenic | Pathogenic | Pathogenic |
APOGEE2 score | 0.973287196910564 | 0.973931315913835 | 0.914608701922158 |
SNPDryad score | 1 | 0.99 | 0.98 |
MutationTaster | disease_causing_automatic | disease_causing_automatic | disease_causing |
MutationTaster score | 1 | 0.58 | 0.52 |
DEOGEN2 score | 0.43 | 0.42 | 0.42 |
Mitoclass.1 | damaging | damaging | damaging |
dbSNP 155 id | rs199476133 | rs199476133 | . |
ClinVar July2022 Variation id | 9642 | 9641 | . |
ClinVar July2022 CLNSIG | Pathogenic | Pathogenic | . |
ClinVar July2022 CLNDN | Leber_optic_atrophy|Leigh_syndrome|Ataxia_and_polyneuropathy,_adult-onset|NARP_syndrome|Mitochondrial_complex_5_(ATP_synthase)_deficiency,_mitochondrial_type_1|Mitochondrial_disease|not_provided | Scrotal_hypoplasia|Hypertelorism|Low-set_ears|Rod-cone_dystrophy|Wide_intermamillary_distance|Leber_optic_atrophy|Postaxial_hand_polydactyly|Cerebellar_ataxia|Premature_birth|Bilateral_cleft_lip_and_palate|Camptodactyly_of_finger|Leigh_syndrome|NARP_syndrome|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:0010781,MedGen:C1838916,OMIM:500010|MONDO:MONDO:0010794,MedGen:C1328349,OMIM:551500,Orphanet:ORPHA644|MONDO:MONDO:0027069,MedGen:C3275684,OMIM:500015|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:ORPHA68380|MedGen:CN517202 | Human_Phenotype_Ontology:HP:0000046,MedGen:C0431659|Human_Phenotype_Ontology:HP:0000316,Human_Phenotype_Ontology:HP:0000578,Human_Phenotype_Ontology:HP:0002001,Human_Phenotype_Ontology:HP:0004657,Human_Phenotype_Ontology:HP:0007871,MedGen:C0020534,OMIM:145400|Human_Phenotype_Ontology:HP:0000369,MedGen:C0239234|Human_Phenotype_Ontology:HP:0000510,Human_Phenotype_Ontology:HP:0001127,Human_Phenotype_Ontology:HP:0007635,Human_Phenotype_Ontology:HP:0007645,Human_Phenotype_Ontology:HP:0007742,Human_Phenotype_Ontology:HP:0007816,Human_Phenotype_Ontology:HP:0007826,Human_Phenotype_Ontology:HP:0007927,Human_Phenotype_Ontology:HP:0008036,MedGen:C4551714|Human_Phenotype_Ontology:HP:0000779,Human_Phenotype_Ontology:HP:0001554,Human_Phenotype_Ontology:HP:0006610,MedGen:C1827524|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:0001162,Human_Phenotype_Ontology:HP:0004698,Human_Phenotype_Ontology:HP:0005763,Human_Phenotype_Ontology:HP:0009984,MONDO:MONDO:0017426,MedGen:C0431904|Human_Phenotype_Ontology:HP:0001251,Human_Phenotype_Ontology:HP:0001253,Human_Phenotype_Ontology:HP:0002513,Human_Phenotype_Ontology:HP:0007050,Human_Phenotype_Ontology:HP:0007157,MONDO:MONDO:0000437,MedGen:C0007758,Orphanet:ORPHA102002,SNOMED_CT:85102008|Human_Phenotype_Ontology:HP:0001622,MedGen:C0151526|Human_Phenotype_Ontology:HP:0002744,MedGen:C1398522|Human_Phenotype_Ontology:HP:0005651,Human_Phenotype_Ontology:HP:0005662,Human_Phenotype_Ontology:HP:0005713,Human_Phenotype_Ontology:HP:0005801,Human_Phenotype_Ontology:HP:0005821,Human_Phenotype_Ontology:HP:0006195,Human_Phenotype_Ontology:HP:0006218,Human_Phenotype_Ontology:HP:0006240,Human_Phenotype_Ontology:HP:0009698,Human_Phenotype_Ontology:HP:0100490,MedGen:C0409348|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:ORPHA506,SNOMED_CT:29570005|MONDO:MONDO:0010794,MedGen:C1328349,OMIM:551500,Orphanet:ORPHA644|MONDO:MONDO:0027069,MedGen:C3275684,OMIM:500015|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:ORPHA68380|MedGen:CN517202 | . |
COSMIC 90 | . | . | . |
MITOMAP Allele | T8993C | T8993G | . |
MITOMAP Disease Het/Hom | -/+ | +/+ | . |
MITOMAP Disease Clinical info | NARP / Leigh Disease / MILS / other | NARP / Leigh Disease / MILS / other | . |
MITOMAP Disease Status | Cfrm [P] | Cfrm [P] | . |
MITOMAP Disease GenBank Freq | 0.003%(0.000%) | 0.010%(0.000%) | . |
MITOMAP Disease GenBank Seqs | 2 (0) | 6 (0) | . |
MITOMAP Disease GenBank Curated refs | 51 | 161 | . |
MITOMAP General GenBank Freq | . | . | . |
MITOMAP General GenBank Seqs | . | . | . |
MITOMAP General Curated refs | . | . | . |
gnomAD 3.1 filter | PASS | npg | . |
gnomAD 3.1 AC Homo | 1 | 0 | . |
gnomAD 3.1 AC Het | 1 | 0 | . |
gnomAD 3.1 AF Hom | 0.000017720757 | 0 | . |
gnomAD 3.1 AF Het | 0.000017720757 | 0 | . |
gnomAD 3.1 AN | 56431 | 56433 | . |
HelixMTdb AC Hom | 0.0 | 0.0 | . |
HelixMTdb AF Hom | 0.0 | 0.0 | . |
HelixMTdb AC Het | 2.0 | 1.0 | . |
HelixMTdb AF Het | 1.0204967e-05 | 5.1024836e-06 | . |
HelixMTdb mean ARF | 0.41236 | 0.59358 | . | HelixMTdb max ARF | 0.5687 | 0.59358 | . |
EVmutation | MT-ATP6_156L|221Y:0.236277;218V:0.185549;163N:0.175304;213V:0.153339;209I:0.108743;205A:0.107658;158V:0.092486;171M:0.084289;173L:0.072801;195I:0.069883;170L:0.06897 | MT-ATP6_156L|221Y:0.236277;218V:0.185549;163N:0.175304;213V:0.153339;209I:0.108743;205A:0.107658;158V:0.092486;171M:0.084289;173L:0.072801;195I:0.069883;170L:0.06897 | MT-ATP6_156L|221Y:0.236277;218V:0.185549;163N:0.175304;213V:0.153339;209I:0.108743;205A:0.107658;158V:0.092486;171M:0.084289;173L:0.072801;195I:0.069883;170L:0.06897 |
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 | . | . | . |