MitImpact id |
MI.1506 |
MI.1505 |
MI.1504 |
Chr |
chrM |
chrM |
chrM |
Start |
8394 |
8394 |
8394 |
Ref |
C |
C |
C |
Alt |
T |
A |
G |
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 |
29 |
29 |
29 |
Gene start |
8366 |
8366 |
8366 |
Gene end |
8572 |
8572 |
8572 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
CCC/CTC |
CCC/CAC |
CCC/CGC |
AA position |
10 |
10 |
10 |
AA ref |
P |
P |
P |
AA alt |
L |
H |
R |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516070 |
516070 |
516070 |
HGVS |
NC_012920.1:g.8394C>T |
NC_012920.1:g.8394C>A |
NC_012920.1:g.8394C>G |
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 |
0.685 |
0.685 |
0.685 |
PhyloP 470Way |
-0.441 |
-0.441 |
-0.441 |
PhastCons 100V |
0 |
0 |
0 |
PhastCons 470Way |
0.002 |
0.002 |
0.002 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1.0 |
1.0 |
1.0 |
SIFT |
neutral |
deleterious |
deleterious |
SIFT score |
1 |
0.02 |
0.01 |
SIFT4G |
Tolerated |
Damaging |
Damaging |
SIFT4G score |
0.463 |
0.031 |
0.029 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.56962521 |
0.47886177 |
0.51005936 |
VEST FDR |
0.85 |
0.85 |
0.85 |
Mitoclass.1 |
neutral |
neutral |
neutral |
SNPDryad |
Neutral |
Neutral |
Neutral |
SNPDryad score |
0.22 |
0.42 |
0.58 |
MutationTaster |
Polymorphism |
Polymorphism |
Polymorphism |
MutationTaster score |
0.999988 |
1 |
1 |
MutationTaster converted rankscore |
0.18198 |
0.08975 |
0.08975 |
MutationTaster model |
simple_aae |
simple_aae |
simple_aae |
MutationTaster AAE |
P10L |
P10H |
P10R |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
2.23 |
1.97 |
1.98 |
fathmm converted rankscore |
0.18083 |
0.22067 |
0.21865 |
AlphaMissense |
likely_benign |
likely_benign |
ambiguous |
AlphaMissense score |
0.1255 |
0.267 |
0.4368 |
CADD |
Neutral |
Deleterious |
Neutral |
CADD score |
1.440867 |
3.661614 |
2.258599 |
CADD phred |
13.0 |
23.2 |
17.89 |
PROVEAN |
Tolerated |
Tolerated |
Tolerated |
PROVEAN score |
0.02 |
-1.42 |
-2.17 |
MutationAssessor |
. |
. |
. |
MutationAssessor score |
. |
. |
. |
EFIN SP |
Neutral |
Neutral |
Neutral |
EFIN SP score |
0.996 |
0.954 |
0.996 |
EFIN HD |
Neutral |
Neutral |
Neutral |
EFIN HD score |
0.942 |
0.44 |
0.448 |
MLC |
Neutral |
Neutral |
Neutral |
MLC score |
0.05612892 |
0.05612892 |
0.05612892 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Neutral |
Neutral |
Pathogenic |
APOGEE1 score |
0.33 |
0.49 |
0.55 |
APOGEE2 |
Benign |
Likely-benign |
Likely-benign |
APOGEE2 score |
0.0080492173818374 |
0.127902798395282 |
0.127138956824646 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1 |
1 |
1 |
Condel |
deleterious |
neutral |
neutral |
Condel score |
0.5 |
0.01 |
0.01 |
COVEC WMV |
neutral |
deleterious |
deleterious |
COVEC WMV score |
-2 |
5 |
5 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.69 |
0.73 |
0.73 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.017594 |
0.053933 |
0.061433 |
DEOGEN2 converted rankscore |
0.14326 |
0.29583 |
0.31651 |
Meta-SNP |
. |
. |
. |
Meta-SNP score |
. |
. |
. |
PolyPhen2 transf |
low impact |
low impact |
low impact |
PolyPhen2 transf score |
-3.6 |
-3.6 |
-3.6 |
SIFT_transf |
high impact |
medium impact |
medium impact |
SIFT transf score |
1.98 |
-0.66 |
-0.84 |
MutationAssessor transf |
medium impact |
medium impact |
medium impact |
MutationAssessor transf score |
-0.92 |
1.01 |
1.01 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.76 |
0.7 |
0.66 |
CHASM FDR |
0.85 |
0.85 |
0.85 |
ClinVar id |
692841.0 |
. |
. |
ClinVar Allele id |
681377.0 |
. |
. |
ClinVar CLNDISDB |
MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 |
. |
. |
ClinVar CLNDN |
Leigh_syndrome |
. |
. |
ClinVar CLNSIG |
Uncertain_significance |
. |
. |
MITOMAP Disease Clinical info |
. |
. |
. |
MITOMAP Disease Status |
. |
. |
. |
MITOMAP Disease Hom/Het |
./. |
./. |
./. |
MITOMAP General GenBank Freq |
0.0065% |
. |
. |
MITOMAP General GenBank Seqs |
4 |
. |
. |
MITOMAP General Curated refs |
. |
. |
. |
MITOMAP Variant Class |
polymorphism |
. |
. |
gnomAD 3.1 AN |
56432.0 |
. |
. |
gnomAD 3.1 AC Homo |
4.0 |
. |
. |
gnomAD 3.1 AF Hom |
7.08818e-05 |
. |
. |
gnomAD 3.1 AC Het |
1.0 |
. |
. |
gnomAD 3.1 AF Het |
1.77204e-05 |
. |
. |
gnomAD 3.1 filter |
PASS |
. |
. |
HelixMTdb AC Hom |
12.0 |
. |
. |
HelixMTdb AF Hom |
6.12298e-05 |
. |
. |
HelixMTdb AC Het |
6.0 |
. |
. |
HelixMTdb AF Het |
3.06149e-05 |
. |
. |
HelixMTdb mean ARF |
0.37584 |
. |
. |
HelixMTdb max ARF |
0.90862 |
. |
. |
ToMMo 54KJPN AC |
. |
. |
. |
ToMMo 54KJPN AF |
. |
. |
. |
ToMMo 54KJPN AN |
. |
. |
. |
COSMIC 90 |
. |
. |
. |
dbSNP 156 id |
rs1603221450 |
. |
. |