MitImpact id |
MI.1508 |
MI.1507 |
MI.1509 |
Chr |
chrM |
chrM |
chrM |
Start |
8396 |
8396 |
8396 |
Ref |
A |
A |
A |
Alt |
G |
C |
T |
Gene symbol |
MT-ATP8 |
MT-ATP8 |
MT-ATP8 |
Extended annotation |
mitochondrially encoded ATP synthase membrane subunit 8 |
mitochondrially encoded ATP synthase membrane subunit 8 |
mitochondrially encoded ATP synthase membrane subunit 8 |
Gene position |
31 |
31 |
31 |
Gene start |
8366 |
8366 |
8366 |
Gene end |
8572 |
8572 |
8572 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
ACC/GCC |
ACC/CCC |
ACC/TCC |
AA position |
11 |
11 |
11 |
AA ref |
T |
T |
T |
AA alt |
A |
P |
S |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516070 |
516070 |
516070 |
HGVS |
NC_012920.1:g.8396A>G |
NC_012920.1:g.8396A>C |
NC_012920.1:g.8396A>T |
HGNC id |
7415 |
7415 |
7415 |
Respiratory Chain complex |
V |
V |
V |
Ensembl gene id |
ENSG00000228253 |
ENSG00000228253 |
ENSG00000228253 |
Ensembl transcript id |
ENST00000361851 |
ENST00000361851 |
ENST00000361851 |
Ensembl protein id |
ENSP00000355265 |
ENSP00000355265 |
ENSP00000355265 |
Uniprot id |
P03928 |
P03928 |
P03928 |
Uniprot name |
ATP8_HUMAN |
ATP8_HUMAN |
ATP8_HUMAN |
Ncbi gene id |
4509 |
4509 |
4509 |
Ncbi protein id |
YP_003024030.1 |
YP_003024030.1 |
YP_003024030.1 |
PhyloP 100V |
-0.605 |
-0.605 |
-0.605 |
PhyloP 470Way |
0.819 |
0.819 |
0.819 |
PhastCons 100V |
0 |
0 |
0 |
PhastCons 470Way |
0.011 |
0.011 |
0.011 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
0.97 |
0.99 |
0.97 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.64 |
0.22 |
0.49 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0.024 |
0.004 |
0.029 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.6294906 |
0.26709301 |
0.52918828 |
VEST FDR |
0.85 |
0.85 |
0.85 |
Mitoclass.1 |
neutral |
neutral |
neutral |
SNPDryad |
Neutral |
Neutral |
Neutral |
SNPDryad score |
0.42 |
0.81 |
0.43 |
MutationTaster |
Polymorphism |
Polymorphism |
Polymorphism |
MutationTaster score |
1 |
1 |
1 |
MutationTaster converted rankscore |
0.08975 |
0.08975 |
0.08975 |
MutationTaster model |
simple_aae |
simple_aae |
simple_aae |
MutationTaster AAE |
T11A |
T11P |
T11S |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
1.86 |
1.78 |
1.84 |
fathmm converted rankscore |
0.24285 |
0.25678 |
0.24656 |
AlphaMissense |
likely_benign |
likely_benign |
likely_benign |
AlphaMissense score |
0.0663 |
0.1408 |
0.1173 |
CADD |
Neutral |
Deleterious |
Neutral |
CADD score |
2.112373 |
2.657259 |
2.501564 |
CADD phred |
16.93 |
20.5 |
19.48 |
PROVEAN |
Tolerated |
Damaging |
Tolerated |
PROVEAN score |
-1.88 |
-3.41 |
-2.12 |
MutationAssessor |
medium |
. |
. |
MutationAssessor score |
2.095 |
. |
. |
EFIN SP |
Neutral |
Neutral |
Neutral |
EFIN SP score |
0.994 |
0.994 |
0.998 |
EFIN HD |
Neutral |
Neutral |
Neutral |
EFIN HD score |
0.638 |
0.34 |
0.632 |
MLC |
Neutral |
Neutral |
Neutral |
MLC score |
0.0526284 |
0.0526284 |
0.0526284 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Neutral |
Neutral |
Neutral |
APOGEE1 score |
0.4 |
0.49 |
0.42 |
APOGEE2 |
Likely-benign |
Likely-benign |
Likely-benign |
APOGEE2 score |
0.105765577190923 |
0.222596817783112 |
0.0792355597054836 |
CAROL |
neutral |
deleterious |
neutral |
CAROL score |
0.97 |
0.99 |
0.97 |
Condel |
neutral |
neutral |
neutral |
Condel score |
0.34 |
0.12 |
0.26 |
COVEC WMV |
neutral |
neutral |
neutral |
COVEC WMV score |
-2 |
-2 |
-2 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.67 |
0.77 |
0.66 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.0372 |
0.072639 |
0.034797 |
DEOGEN2 converted rankscore |
0.24386 |
0.34504 |
0.23466 |
Meta-SNP |
. |
. |
. |
Meta-SNP score |
. |
. |
. |
PolyPhen2 transf |
low impact |
low impact |
low impact |
PolyPhen2 transf score |
-2.19 |
-2.65 |
-2.19 |
SIFT_transf |
medium impact |
medium impact |
medium impact |
SIFT transf score |
0.43 |
-0.02 |
0.28 |
MutationAssessor transf |
medium impact |
medium impact |
medium impact |
MutationAssessor transf score |
0.55 |
0.25 |
0.07 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.53 |
0.62 |
0.72 |
CHASM FDR |
0.85 |
0.85 |
0.85 |
ClinVar id |
692842.0 |
. |
. |
ClinVar Allele id |
681378.0 |
. |
. |
ClinVar CLNDISDB |
MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 |
. |
. |
ClinVar CLNDN |
Leigh_syndrome |
. |
. |
ClinVar CLNSIG |
Benign |
. |
. |
MITOMAP Disease Clinical info |
. |
. |
. |
MITOMAP Disease Status |
. |
. |
. |
MITOMAP Disease Hom/Het |
./. |
./. |
./. |
MITOMAP General GenBank Freq |
0.1685% |
. |
0.0% |
MITOMAP General GenBank Seqs |
103 |
. |
0 |
MITOMAP General Curated refs |
19340307;19188198;15804362;18691441;24456990 |
. |
. |
MITOMAP Variant Class |
polymorphism |
. |
polymorphism |
gnomAD 3.1 AN |
56433.0 |
. |
. |
gnomAD 3.1 AC Homo |
37.0 |
. |
. |
gnomAD 3.1 AF Hom |
0.000655645 |
. |
. |
gnomAD 3.1 AC Het |
0.0 |
. |
. |
gnomAD 3.1 AF Het |
0.0 |
. |
. |
gnomAD 3.1 filter |
PASS |
. |
. |
HelixMTdb AC Hom |
72.0 |
. |
1.0 |
HelixMTdb AF Hom |
0.00036737882 |
. |
5.1024836e-06 |
HelixMTdb AC Het |
1.0 |
. |
0.0 |
HelixMTdb AF Het |
5.1024836e-06 |
. |
0.0 |
HelixMTdb mean ARF |
0.22581 |
. |
. |
HelixMTdb max ARF |
0.22581 |
. |
. |
ToMMo 54KJPN AC |
4 |
. |
. |
ToMMo 54KJPN AF |
7.4e-05 |
. |
. |
ToMMo 54KJPN AN |
54302 |
. |
. |
COSMIC 90 |
. |
. |
. |
dbSNP 156 id |
rs1603221454 |
. |
. |