MitImpact id |
MI.1401 |
MI.1403 |
MI.1402 |
Chr |
chrM |
chrM |
chrM |
Start |
9185 |
9185 |
9185 |
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 |
659 |
659 |
659 |
Gene start |
8527 |
8527 |
8527 |
Gene end |
9207 |
9207 |
9207 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
CTC/CCC |
CTC/CAC |
CTC/CGC |
AA position |
220 |
220 |
220 |
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.9185T>C |
NC_012920.1:g.9185T>A |
NC_012920.1:g.9185T>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 |
7.687 |
7.687 |
7.687 |
PhyloP 470Way |
0.742 |
0.742 |
0.742 |
PhastCons 100V |
0.986 |
0.986 |
0.986 |
PhastCons 470Way |
0.701 |
0.701 |
0.701 |
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 |
0.2 |
0.22 |
0.19 |
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 automatic |
Disease |
Disease |
MutationTaster score |
1.0 |
0.999996 |
0.999998 |
MutationTaster converted rankscore |
0.81001 |
0.58761 |
0.58761 |
MutationTaster model |
simple_aae |
simple_aae |
simple_aae |
MutationTaster AAE |
L220P |
L220H |
L220R |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
4.14 |
4.14 |
4.15 |
fathmm converted rankscore |
0.02839 |
0.02839 |
0.02815 |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.9687 |
0.8652 |
0.7344 |
CADD |
Deleterious |
Deleterious |
Deleterious |
CADD score |
3.986474 |
4.222825 |
4.316557 |
CADD phred |
23.6 |
23.9 |
24.0 |
PROVEAN |
Damaging |
Damaging |
Damaging |
PROVEAN score |
-6.22 |
-6.2 |
-5.32 |
MutationAssessor |
high |
high |
high |
MutationAssessor score |
5.285 |
5.285 |
5.285 |
EFIN SP |
Damaging |
Damaging |
Damaging |
EFIN SP score |
0.202 |
0.378 |
0.152 |
EFIN HD |
Neutral |
Neutral |
Neutral |
EFIN HD score |
0.422 |
0.384 |
0.344 |
MLC |
Neutral |
Neutral |
Neutral |
MLC score |
0.08002897 |
0.08002897 |
0.08002897 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Pathogenic |
Pathogenic |
Pathogenic |
APOGEE1 score |
0.94 |
0.66 |
0.95 |
APOGEE2 |
Likely-pathogenic |
Likely-pathogenic |
VUS+ |
APOGEE2 score |
0.904565643418929 |
0.810281980867029 |
0.569699360876384 |
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 |
0.321284 |
0.321284 |
0.313807 |
DEOGEN2 converted rankscore |
0.69240 |
0.69240 |
0.68553 |
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 |
2.59 |
2.59 |
2.59 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.48 |
0.58 |
0.54 |
CHASM FDR |
0.9 |
0.9 |
0.9 |
ClinVar id |
9647.0 |
. |
. |
ClinVar Allele id |
24686.0 |
. |
. |
ClinVar CLNDISDB |
MONDO:MONDO:0027069,MedGen:C3275684,OMIM:500015|MONDO:MONDO:0015626,MedGen:C0007959,OMIM:PS118220,Orphanet:166|MedGen:CN517202|MedGen:CN043634|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104|MONDO:MONDO:0007309,MedGen:C0270911,OMIM:118220,Orphanet:101081 |
. |
. |
ClinVar CLNDN |
Mitochondrial_complex_5_(ATP_synthase)_deficiency,_mitochondrial_type_1|Charcot-Marie-Tooth_disease|not_provided|Mitochondrial_DNA-Associated_Leigh_Syndrome_and_NARP|Mitochondrial_disease|Leigh_syndrome|Leber_optic_atrophy|Charcot-Marie-Tooth_disease,_type_IA |
. |
. |
ClinVar CLNSIG |
Pathogenic |
. |
. |
MITOMAP Disease Clinical info |
Leigh Disease / Ataxia syndromes / NARP-like disease / Episodic weakness and Charcot-Marie-Tooth |
. |
. |
MITOMAP Disease Status |
Cfrm [P] |
. |
. |
MITOMAP Disease Hom/Het |
+/+ |
./. |
./. |
MITOMAP General GenBank Freq |
0.0049% |
0.0016% |
0.0098% |
MITOMAP General GenBank Seqs |
3 |
1 |
6 |
MITOMAP General Curated refs |
25548692;22933740;19747204;28429146;29467576;30461153;37737178;30128709;27290639;29116603;22577227;17352390;24316278;24153443;32042921;23847141;30763462;31187502;32858252;33717984;29253894;29228836;28132834;34329598;36137325;21473984;31996241;28754700;16217706;18620007;27783406;20546952;18461509;29756269;21457906;31500933 |
. |
. |
MITOMAP Variant Class |
disease |
polymorphism |
polymorphism |
gnomAD 3.1 AN |
56421.0 |
. |
56431.0 |
gnomAD 3.1 AC Homo |
0.0 |
. |
2.0 |
gnomAD 3.1 AF Hom |
0.0 |
. |
3.54415e-05 |
gnomAD 3.1 AC Het |
2.0 |
. |
1.0 |
gnomAD 3.1 AF Het |
3.54478e-05 |
. |
1.77208e-05 |
gnomAD 3.1 filter |
PASS |
. |
PASS |
HelixMTdb AC Hom |
0.0 |
. |
15.0 |
HelixMTdb AF Hom |
0.0 |
. |
7.653725e-05 |
HelixMTdb AC Het |
2.0 |
. |
3.0 |
HelixMTdb AF Het |
1.0204967e-05 |
. |
1.530745e-05 |
HelixMTdb mean ARF |
0.43429 |
. |
0.36981 |
HelixMTdb max ARF |
0.45192 |
. |
0.85025 |
ToMMo 54KJPN AC |
1 |
. |
14 |
ToMMo 54KJPN AF |
1.8e-05 |
. |
0.000258 |
ToMMo 54KJPN AN |
54302 |
. |
54302 |
COSMIC 90 |
. |
. |
. |
dbSNP 156 id |
rs199476138 |
. |
rs199476138 |