MitImpact id |
MI.689 |
MI.690 |
Chr |
chrM |
chrM |
Start |
8851 |
8851 |
Ref |
T |
T |
Alt |
C |
G |
Gene symbol |
MT-ATP6 |
MT-ATP6 |
Extended annotation |
mitochondrially encoded ATP synthase membrane subunit 6 |
mitochondrially encoded ATP synthase membrane subunit 6 |
Gene position |
325 |
325 |
Gene start |
8527 |
8527 |
Gene end |
9207 |
9207 |
Gene strand |
+ |
+ |
Codon substitution |
TGA/CGA |
TGA/GGA |
AA position |
109 |
109 |
AA ref |
W |
W |
AA alt |
R |
G |
Functional effect general |
missense |
missense |
Functional effect detailed |
missense |
missense |
OMIM id |
516060 |
516060 |
HGVS |
NC_012920.1:g.8851T>C |
NC_012920.1:g.8851T>G |
HGNC id |
7414 |
7414 |
Respiratory Chain complex |
V |
V |
Ensembl gene id |
ENSG00000198899 |
ENSG00000198899 |
Ensembl transcript id |
ENST00000361899 |
ENST00000361899 |
Ensembl protein id |
ENSP00000354632 |
ENSP00000354632 |
Uniprot id |
P00846 |
P00846 |
Uniprot name |
ATP6_HUMAN |
ATP6_HUMAN |
Ncbi gene id |
4508 |
4508 |
Ncbi protein id |
YP_003024031.1 |
YP_003024031.1 |
PhyloP 100V |
5.983 |
5.983 |
PhyloP 470Way |
0.666 |
0.666 |
PhastCons 100V |
1 |
1 |
PhastCons 470Way |
0.736 |
0.736 |
PolyPhen2 |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1.0 |
0.99 |
SIFT |
deleterious |
deleterious |
SIFT score |
0 |
0 |
SIFT4G |
Damaging |
Damaging |
SIFT4G score |
0.0 |
0.0 |
VEST |
Neutral |
Neutral |
VEST pvalue |
0.28 |
0.24 |
VEST FDR |
0.65 |
0.65 |
Mitoclass.1 |
damaging |
damaging |
SNPDryad |
Pathogenic |
Pathogenic |
SNPDryad score |
0.97 |
1 |
MutationTaster |
. |
. |
MutationTaster score |
. |
. |
MutationTaster converted rankscore |
. |
. |
MutationTaster model |
. |
. |
MutationTaster AAE |
. |
. |
fathmm |
. |
. |
fathmm score |
. |
. |
fathmm converted rankscore |
. |
. |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.987 |
0.8008 |
CADD |
Deleterious |
Deleterious |
CADD score |
3.556674 |
3.870712 |
CADD phred |
23.1 |
23.5 |
PROVEAN |
Damaging |
Damaging |
PROVEAN score |
-12.92 |
-11.98 |
MutationAssessor |
. |
high |
MutationAssessor score |
. |
5.32 |
EFIN SP |
Damaging |
Neutral |
EFIN SP score |
0.414 |
0.618 |
EFIN HD |
Damaging |
Neutral |
EFIN HD score |
0.254 |
0.416 |
MLC |
Neutral |
Neutral |
MLC score |
0.04828294 |
0.04828294 |
PANTHER score |
. |
. |
PhD-SNP score |
. |
. |
APOGEE1 |
Pathogenic |
Neutral |
APOGEE1 score |
0.69 |
0.5 |
APOGEE2 |
Likely-pathogenic |
Likely-pathogenic |
APOGEE2 score |
0.867435890954745 |
0.72895471332079 |
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 |
DEOGEN2 |
. |
. |
DEOGEN2 score |
. |
. |
DEOGEN2 converted rankscore |
. |
. |
Meta-SNP |
. |
. |
Meta-SNP score |
. |
. |
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 |
Neutral |
Neutral |
CHASM pvalue |
0.24 |
0.28 |
CHASM FDR |
0.9 |
0.9 |
ClinVar id |
9645.0 |
. |
ClinVar Allele id |
24684.0 |
. |
ClinVar CLNDISDB |
MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|MONDO:MONDO:0010774,MedGen:C1839022,OMIM:500003|MedGen:CN517202|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 |
. |
ClinVar CLNDN |
Mitochondrial_disease|Striatonigral_degeneration,_infantile,_mitochondrial|not_provided|Leber_optic_atrophy|Leigh_syndrome |
. |
ClinVar CLNSIG |
Uncertain_significance |
. |
MITOMAP Disease Clinical info |
BSN / Leigh syndrome |
. |
MITOMAP Disease Status |
Cfrm [VUS*] |
. |
MITOMAP Disease Hom/Het |
+/+ |
./. |
MITOMAP General GenBank Freq |
0.0065% |
. |
MITOMAP General GenBank Seqs |
4 |
. |
MITOMAP General Curated refs |
18620007;23206802;24002810;21470976;30763462;21457906;8554662;29253894;32652755 |
. |
MITOMAP Variant Class |
disease |
. |
gnomAD 3.1 AN |
56428.0 |
56433.0 |
gnomAD 3.1 AC Homo |
2.0 |
0.0 |
gnomAD 3.1 AF Hom |
3.54434e-05 |
0.0 |
gnomAD 3.1 AC Het |
0.0 |
0.0 |
gnomAD 3.1 AF Het |
0.0 |
0.0 |
gnomAD 3.1 filter |
PASS |
npg |
HelixMTdb AC Hom |
10.0 |
. |
HelixMTdb AF Hom |
5.1024836e-05 |
. |
HelixMTdb AC Het |
4.0 |
. |
HelixMTdb AF Het |
2.0409934e-05 |
. |
HelixMTdb mean ARF |
0.29899 |
. |
HelixMTdb max ARF |
0.59701 |
. |
ToMMo 54KJPN AC |
1 |
. |
ToMMo 54KJPN AF |
1.8e-05 |
. |
ToMMo 54KJPN AN |
54302 |
. |
COSMIC 90 |
. |
. |
dbSNP 156 id |
. |
. |