MitImpact id |
MI.1085 |
MI.1083 |
MI.1084 |
Chr |
chrM |
chrM |
chrM |
Start |
9035 |
9035 |
9035 |
Ref |
T |
T |
T |
Alt |
C |
A |
G |
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 |
509 |
509 |
509 |
Gene start |
8527 |
8527 |
8527 |
Gene end |
9207 |
9207 |
9207 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
CTC/CCC |
CTC/CAC |
CTC/CGC |
AA position |
170 |
170 |
170 |
AA ref |
L |
L |
L |
AA alt |
P |
H |
R |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516060 |
516060 |
516060 |
HGVS |
NC_012920.1:g.9035T>C |
NC_012920.1:g.9035T>A |
NC_012920.1:g.9035T>G |
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 |
7.713 |
7.713 |
7.713 |
PhyloP 470Way |
0.742 |
0.742 |
0.742 |
PhastCons 100V |
0.972 |
0.972 |
0.972 |
PhastCons 470Way |
0.102 |
0.102 |
0.102 |
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 |
0.0 |
0.0 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.17 |
0.16 |
0.16 |
VEST FDR |
0.65 |
0.65 |
0.65 |
Mitoclass.1 |
damaging |
damaging |
damaging |
SNPDryad |
Pathogenic |
Pathogenic |
Pathogenic |
SNPDryad score |
1 |
0.97 |
0.99 |
MutationTaster |
Disease |
Polymorphism |
Polymorphism |
MutationTaster score |
0.987975 |
0.998904 |
0.997988 |
MutationTaster converted rankscore |
0.40682 |
0.2181 |
0.22411 |
MutationTaster model |
simple_aae |
simple_aae |
simple_aae |
MutationTaster AAE |
L170P |
L170H |
L170R |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
3.87 |
3.87 |
3.88 |
fathmm converted rankscore |
0.03597 |
0.03597 |
0.03570 |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.975 |
0.9807 |
0.9609 |
CADD |
Deleterious |
Deleterious |
Deleterious |
CADD score |
4.034776 |
4.324693 |
4.246721 |
CADD phred |
23.7 |
24.0 |
23.9 |
PROVEAN |
Damaging |
Damaging |
Damaging |
PROVEAN score |
-6.22 |
-6.17 |
-5.29 |
MutationAssessor |
high |
high |
high |
MutationAssessor score |
5.28 |
5.28 |
5.28 |
EFIN SP |
Damaging |
Damaging |
Damaging |
EFIN SP score |
0.284 |
0.474 |
0.37 |
EFIN HD |
Damaging |
Damaging |
Damaging |
EFIN HD score |
0.148 |
0.138 |
0.13 |
MLC |
Neutral |
Neutral |
Neutral |
MLC score |
0.1125596 |
0.1125596 |
0.1125596 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Pathogenic |
Neutral |
Pathogenic |
APOGEE1 score |
0.78 |
0.4 |
0.56 |
APOGEE2 |
Pathogenic |
Likely-pathogenic |
Pathogenic |
APOGEE2 score |
0.977459277270844 |
0.874524974230017 |
0.946570512202185 |
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 |
0.89 |
0.87 |
0.9 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.320359 |
0.320359 |
0.312881 |
DEOGEN2 converted rankscore |
0.69156 |
0.69156 |
0.68467 |
Meta-SNP |
. |
. |
. |
Meta-SNP score |
. |
. |
. |
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 |
2.72 |
2.72 |
2.72 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.69 |
0.52 |
0.51 |
CHASM FDR |
0.9 |
0.9 |
0.9 |
ClinVar id |
690280.0 |
. |
. |
ClinVar Allele id |
677959.0 |
. |
. |
ClinVar CLNDISDB |
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|.|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|Human_Phenotype_Ontology:HP:0001329,Human_Phenotype_Ontology:HP:0002073,Human_Phenotype_Ontology:HP:0002496,Human_Phenotype_Ontology:HP:0007331,MedGen:C0393525|. |
. |
. |
ClinVar CLNDN |
Leber_optic_atrophy|Leigh_syndrome|MT-ATP6-related_primary_mitochondrial_disease|Mitochondrial_disease|Progressive_cerebellar_ataxia|See_cases |
. |
. |
ClinVar CLNSIG |
Likely_pathogenic |
. |
. |
MITOMAP Disease Clinical info |
Ataxia syndromes |
. |
. |
MITOMAP Disease Status |
Cfrm [LP] |
. |
. |
MITOMAP Disease Hom/Het |
+/+ |
./. |
./. |
MITOMAP General GenBank Freq |
0.0% |
. |
. |
MITOMAP General GenBank Seqs |
0 |
. |
. |
MITOMAP General Curated refs |
30763462;29467576;19626676;32858252;31187502;22577227 |
. |
. |
MITOMAP Variant Class |
disease |
. |
. |
gnomAD 3.1 AN |
56423.0 |
. |
. |
gnomAD 3.1 AC Homo |
0.0 |
. |
. |
gnomAD 3.1 AF Hom |
0.0 |
. |
. |
gnomAD 3.1 AC Het |
2.0 |
. |
. |
gnomAD 3.1 AF Het |
3.54465e-05 |
. |
. |
gnomAD 3.1 filter |
PASS |
. |
. |
HelixMTdb AC Hom |
0.0 |
. |
. |
HelixMTdb AF Hom |
0.0 |
. |
. |
HelixMTdb AC Het |
8.0 |
. |
. |
HelixMTdb AF Het |
4.081987e-05 |
. |
. |
HelixMTdb mean ARF |
0.25609 |
. |
. |
HelixMTdb max ARF |
0.5098 |
. |
. |
ToMMo 54KJPN AC |
. |
. |
. |
ToMMo 54KJPN AF |
. |
. |
. |
ToMMo 54KJPN AN |
. |
. |
. |
COSMIC 90 |
. |
. |
. |
dbSNP 156 id |
rs1603222000 |
. |
. |