M-8969-G-C
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Mitomap GenBank:
𝑓 0.0 ( AC: 0 )
Consequence
ATP6
missense
missense
Scores
Apogee2
Pathogenic
Clinical Significance
Not reported in ClinVar
Mitochondrial-myopathy+-lactic-acidosis-and-sideroblastic-anemia-(MLASA)-/-IgG-nephropathy,Suspected-mito-disease
Conservation
PhyloP100: 9.61
Genes affected
ATP6 (HGNC:7414): (mitochondrially encoded ATP synthase 6) Contributes to proton-transporting ATP synthase activity, rotational mechanism. Involved in mitochondrial ATP synthesis coupled proton transport. Part of mitochondrial proton-transporting ATP synthase complex. Implicated in Leber hereditary optic neuropathy; NARP syndrome; Parkinson's disease; multiple sclerosis; and systemic lupus erythematosus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very low frequency in mitomap database: 0.0
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP6 | unassigned_transcript_4805 | c.443G>C | p.Ser148Thr | missense_variant | Exon 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|
Frequencies
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
AC:
0
Gnomad homoplasmic
AF:
AC:
3
AN:
56433
Gnomad heteroplasmic
AF:
AC:
1
AN:
56433
Mitomap
Mitochondrial-myopathy+-lactic-acidosis-and-sideroblastic-anemia-(MLASA)-/-IgG-nephropathy,Suspected-mito-disease
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Apogee2
Pathogenic
Hmtvar
Pathogenic
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
DEOGEN2
Benign
T
LIST_S2
Benign
T
MutationAssessor
Pathogenic
H
PROVEAN
Uncertain
D
Sift4G
Pathogenic
D
GERP RS
Varity_R
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at