MitImpact id |
MI.1340 |
MI.1339 |
MI.1341 |
Chr |
chrM |
chrM |
chrM |
Start |
9155 |
9155 |
9155 |
Ref |
A |
A |
A |
Alt |
G |
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 |
629 |
629 |
629 |
Gene start |
8527 |
8527 |
8527 |
Gene end |
9207 |
9207 |
9207 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
CAA/CGA |
CAA/CCA |
CAA/CTA |
AA position |
210 |
210 |
210 |
AA ref |
Q |
Q |
Q |
AA alt |
R |
P |
L |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516060 |
516060 |
516060 |
HGVS |
NC_012920.1:g.9155A>G |
NC_012920.1:g.9155A>C |
NC_012920.1:g.9155A>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 |
8.91 |
8.91 |
8.91 |
PhyloP 470Way |
0.929 |
0.929 |
0.929 |
PhastCons 100V |
1 |
1 |
1 |
PhastCons 470Way |
0.762 |
0.762 |
0.762 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
0.97 |
0.98 |
0.97 |
SIFT |
deleterious |
deleterious |
deleterious |
SIFT score |
0 |
0 |
0 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0.0 |
0.001 |
0.0 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.21 |
0.14 |
0.15 |
VEST FDR |
0.65 |
0.65 |
0.65 |
Mitoclass.1 |
damaging |
damaging |
damaging |
SNPDryad |
Pathogenic |
Pathogenic |
Pathogenic |
SNPDryad score |
0.91 |
0.98 |
0.99 |
MutationTaster |
Disease |
Disease |
Disease |
MutationTaster score |
1.0 |
1.0 |
1.0 |
MutationTaster converted rankscore |
0.81001 |
0.81001 |
0.81001 |
MutationTaster model |
simple_aae |
simple_aae |
simple_aae |
MutationTaster AAE |
Q210R |
Q210P |
Q210L |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
3.02 |
2.98 |
2.99 |
fathmm converted rankscore |
0.08986 |
0.09356 |
0.09262 |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.9228 |
0.9156 |
0.9337 |
CADD |
Deleterious |
Deleterious |
Deleterious |
CADD score |
3.540394 |
3.494531 |
3.937839 |
CADD phred |
23.1 |
23.1 |
23.5 |
PROVEAN |
Damaging |
Damaging |
Damaging |
PROVEAN score |
-3.54 |
-5.34 |
-6.19 |
MutationAssessor |
high |
high |
high |
MutationAssessor score |
5.335 |
4.99 |
5.335 |
EFIN SP |
Damaging |
Damaging |
Neutral |
EFIN SP score |
0.586 |
0.53 |
0.628 |
EFIN HD |
Damaging |
Damaging |
Damaging |
EFIN HD score |
0.138 |
0.15 |
0.126 |
MLC |
Neutral |
Neutral |
Neutral |
MLC score |
0.11096023 |
0.11096023 |
0.11096023 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Pathogenic |
Neutral |
Neutral |
APOGEE1 score |
0.53 |
0.46 |
0.47 |
APOGEE2 |
Likely-pathogenic |
Likely-pathogenic |
Likely-pathogenic |
APOGEE2 score |
0.869336052668355 |
0.830731688266146 |
0.821884211239122 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1 |
1 |
1 |
Condel |
neutral |
neutral |
neutral |
Condel score |
0.02 |
0.01 |
0.02 |
COVEC WMV |
deleterious |
deleterious |
deleterious |
COVEC WMV score |
6 |
6 |
6 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.92 |
0.94 |
0.9 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.422359 |
0.424174 |
0.431689 |
DEOGEN2 converted rankscore |
0.77346 |
0.77469 |
0.77972 |
Meta-SNP |
. |
. |
. |
Meta-SNP score |
. |
. |
. |
PolyPhen2 transf |
low impact |
low impact |
low impact |
PolyPhen2 transf score |
-2.19 |
-2.36 |
-2.19 |
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 |
2.54 |
2.84 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.48 |
0.49 |
0.35 |
CHASM FDR |
0.9 |
0.9 |
0.9 |
ClinVar id |
986472.0 |
. |
. |
ClinVar Allele id |
974623.0 |
. |
. |
ClinVar CLNDISDB |
MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380 |
. |
. |
ClinVar CLNDN |
Leigh_syndrome|Mitochondrial_disease |
. |
. |
ClinVar CLNSIG |
Likely_pathogenic |
. |
. |
MITOMAP Disease Clinical info |
MIDD, renal insufficiency |
. |
Developmental delay, intellectual disability, low citrilline |
MITOMAP Disease Status |
Cfrm [LP] |
. |
Reported |
MITOMAP Disease Hom/Het |
-/+ |
./. |
+/+ |
MITOMAP General GenBank Freq |
0.0% |
. |
0.0% |
MITOMAP General GenBank Seqs |
0 |
. |
0 |
MITOMAP General Curated refs |
34961688;27450679;27966441 |
. |
29307858 |
MITOMAP Variant Class |
disease |
. |
polymorphism;disease |
gnomAD 3.1 AN |
. |
. |
. |
gnomAD 3.1 AC Homo |
. |
. |
. |
gnomAD 3.1 AF Hom |
. |
. |
. |
gnomAD 3.1 AC Het |
. |
. |
. |
gnomAD 3.1 AF Het |
. |
. |
. |
gnomAD 3.1 filter |
. |
. |
. |
HelixMTdb AC Hom |
. |
. |
2.0 |
HelixMTdb AF Hom |
. |
. |
1.0204967e-05 |
HelixMTdb AC Het |
. |
. |
0.0 |
HelixMTdb AF Het |
. |
. |
0.0 |
HelixMTdb mean ARF |
. |
. |
. |
HelixMTdb max ARF |
. |
. |
. |
ToMMo 54KJPN AC |
. |
. |
. |
ToMMo 54KJPN AF |
. |
. |
. |
ToMMo 54KJPN AN |
. |
. |
. |
COSMIC 90 |
. |
. |
. |
dbSNP 156 id |
. |
. |
. |