MitImpact id |
MI.946 |
MI.945 |
MI.947 |
Chr |
chrM |
chrM |
chrM |
Start |
8969 |
8969 |
8969 |
Ref |
G |
G |
G |
Alt |
A |
C |
T |
Gene symbol |
MT-ATP6 |
MT-ATP6 |
MT-ATP6 |
Extended annotation |
mitochondrially encoded ATP synthase membrane subunit 6 |
mitochondrially encoded ATP synthase membrane subunit 6 |
mitochondrially encoded ATP synthase membrane subunit 6 |
Gene position |
443 |
443 |
443 |
Gene start |
8527 |
8527 |
8527 |
Gene end |
9207 |
9207 |
9207 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
AGC/AAC |
AGC/ACC |
AGC/ATC |
AA position |
148 |
148 |
148 |
AA ref |
S |
S |
S |
AA alt |
N |
T |
I |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516060 |
516060 |
516060 |
HGVS |
NC_012920.1:g.8969G>A |
NC_012920.1:g.8969G>C |
NC_012920.1:g.8969G>T |
HGNC id |
7414 |
7414 |
7414 |
Respiratory Chain complex |
V |
V |
V |
Ensembl gene id |
ENSG00000198899 |
ENSG00000198899 |
ENSG00000198899 |
Ensembl transcript id |
ENST00000361899 |
ENST00000361899 |
ENST00000361899 |
Ensembl protein id |
ENSP00000354632 |
ENSP00000354632 |
ENSP00000354632 |
Uniprot id |
P00846 |
P00846 |
P00846 |
Uniprot name |
ATP6_HUMAN |
ATP6_HUMAN |
ATP6_HUMAN |
Ncbi gene id |
4508 |
4508 |
4508 |
Ncbi protein id |
YP_003024031.1 |
YP_003024031.1 |
YP_003024031.1 |
PhyloP 100V |
9.61 |
9.61 |
9.61 |
PhyloP 470Way |
0.965 |
0.965 |
0.965 |
PhastCons 100V |
1 |
1 |
1 |
PhastCons 470Way |
0.247 |
0.247 |
0.247 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
0.98 |
0.98 |
0.99 |
SIFT |
deleterious |
deleterious |
deleterious |
SIFT score |
0 |
0 |
0 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0.0 |
0.0 |
0.0 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.45 |
0.22 |
0.2 |
VEST FDR |
0.65 |
0.65 |
0.65 |
Mitoclass.1 |
damaging |
damaging |
damaging |
SNPDryad |
Neutral |
Neutral |
Pathogenic |
SNPDryad score |
0.88 |
0.67 |
1 |
MutationTaster |
Disease automatic |
Disease |
Disease |
MutationTaster score |
0.999997 |
0.999996 |
1.0 |
MutationTaster converted rankscore |
0.58761 |
0.58761 |
0.81001 |
MutationTaster model |
simple_aae |
simple_aae |
simple_aae |
MutationTaster AAE |
S148N |
S148T |
S148I |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
3.56 |
3.56 |
3.49 |
fathmm converted rankscore |
0.04696 |
0.04696 |
0.05071 |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.8997 |
0.7282 |
0.9357 |
CADD |
Deleterious |
Deleterious |
Deleterious |
CADD score |
3.628728 |
3.455574 |
4.157163 |
CADD phred |
23.2 |
23.0 |
23.8 |
PROVEAN |
Damaging |
Damaging |
Damaging |
PROVEAN score |
-2.76 |
-2.72 |
-5.48 |
MutationAssessor |
high |
high |
high |
MutationAssessor score |
5.335 |
5.335 |
5.335 |
EFIN SP |
Damaging |
Damaging |
Damaging |
EFIN SP score |
0.47 |
0.514 |
0.492 |
EFIN HD |
Damaging |
Damaging |
Damaging |
EFIN HD score |
0.066 |
0.076 |
0.06 |
MLC |
Neutral |
Neutral |
Neutral |
MLC score |
0.01822681 |
0.01822681 |
0.01822681 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Pathogenic |
Neutral |
Neutral |
APOGEE1 score |
0.57 |
0.5 |
0.48 |
APOGEE2 |
Likely-pathogenic |
VUS+ |
Likely-pathogenic |
APOGEE2 score |
0.837553028217724 |
0.67452196329104 |
0.781604418900294 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1 |
1 |
1 |
Condel |
neutral |
neutral |
neutral |
Condel score |
0.01 |
0.01 |
0.01 |
COVEC WMV |
deleterious |
deleterious |
deleterious |
COVEC WMV score |
6 |
6 |
6 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.81 |
0.82 |
0.86 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.331145 |
0.218647 |
0.422588 |
DEOGEN2 converted rankscore |
0.70125 |
0.58143 |
0.77361 |
Meta-SNP |
. |
. |
. |
Meta-SNP score |
. |
. |
. |
PolyPhen2 transf |
low impact |
low impact |
low impact |
PolyPhen2 transf score |
-2.36 |
-2.36 |
-2.65 |
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 |
2.84 |
2.36 |
2.84 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.44 |
0.71 |
0.68 |
CHASM FDR |
0.9 |
0.9 |
0.9 |
ClinVar id |
191364.0 |
. |
. |
ClinVar Allele id |
189167.0 |
. |
. |
ClinVar CLNDISDB |
Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104|MONDO:MONDO:0010789,MedGen:C0162671,OMIM:540000,Orphanet:550|MONDO:MONDO:0010782,MedGen:C4225415,OMIM:500011,Orphanet:2598|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380 |
. |
. |
ClinVar CLNDN |
Leber_optic_atrophy|Juvenile_myopathy,_encephalopathy,_lactic_acidosis_AND_stroke|Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_3|Mitochondrial_disease |
. |
. |
ClinVar CLNSIG |
Likely_pathogenic |
. |
. |
MITOMAP Disease Clinical info |
Mitochondrial myopathy, lactic acidosis and sideroblastic anemia (MLASA) / IgG nephropathy |
Suspected mito disease |
. |
MITOMAP Disease Status |
Cfrm [LP] |
Reported |
. |
MITOMAP Disease Hom/Het |
-/+ |
nr/nr |
./. |
MITOMAP General GenBank Freq |
0.0016% |
0.0% |
. |
MITOMAP General GenBank Seqs |
1 |
0 |
. |
MITOMAP General Curated refs |
37988592;34732400;29350304;27450679;27812026;30763462;25037980 |
32858252 |
. |
MITOMAP Variant Class |
disease |
polymorphism;disease |
. |
gnomAD 3.1 AN |
56424.0 |
56433.0 |
. |
gnomAD 3.1 AC Homo |
0.0 |
3.0 |
. |
gnomAD 3.1 AF Hom |
0.0 |
5.31604e-05 |
. |
gnomAD 3.1 AC Het |
4.0 |
1.0 |
. |
gnomAD 3.1 AF Het |
7.08918e-05 |
1.77201e-05 |
. |
gnomAD 3.1 filter |
PASS |
PASS |
. |
HelixMTdb AC Hom |
0.0 |
8.0 |
. |
HelixMTdb AF Hom |
0.0 |
4.081987e-05 |
. |
HelixMTdb AC Het |
9.0 |
2.0 |
. |
HelixMTdb AF Het |
4.5922352e-05 |
1.0204967e-05 |
. |
HelixMTdb mean ARF |
0.13062 |
0.37364 |
. |
HelixMTdb max ARF |
0.32634 |
0.52688 |
. |
ToMMo 54KJPN AC |
. |
1 |
. |
ToMMo 54KJPN AF |
. |
1.8e-05 |
. |
ToMMo 54KJPN AN |
. |
54302 |
. |
COSMIC 90 |
. |
. |
. |
dbSNP 156 id |
rs794726857 |
rs794726857 |
. |