rs1556423437
Positions:
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The ENST00000361851.1(MT-ATP8):c.17C>T(p.Thr6Ile) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Mitomap GenBank:
𝑓 0.00010 ( AC: 9 )
Consequence
MT-ATP8
ENST00000361851.1 missense
ENST00000361851.1 missense
Scores
Apogee2
Benign
Clinical Significance
Suspected-mito-disease
Conservation
PhyloP100: 4.78
Genes affected
MT-ATP8 (HGNC:7415): (mitochondrially encoded ATP synthase 8) 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 multiple sclerosis and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP4
?
Apogee2 supports a benign effect, 0.10092881 < 0.5 .
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP8 | ATP8.1 use as main transcript | c.17C>T | p.Thr6Ile | missense_variant | 1/1 | ||
TRNK | TRNK.1 use as main transcript | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-ATP8 | ENST00000361851.1 | c.17C>T | p.Thr6Ile | missense_variant | 1/1 | P1 | |||
MT-TK | ENST00000387421.1 | downstream_gene_variant |
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:
9
Gnomad homoplasmic
AF:
AC:
3
AN:
56431
Gnomad heteroplasmic
AF:
AC:
0
AN:
56431
Alfa
AF:
Hom.:
Mitomap
Suspected-mito-disease
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Leigh syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Oct 17, 2019 | The NC_012920.1:m.8382C>T (YP_003024030.1:p.Thr6Ile) variant in MTATP8 gene is interpretated to be a Uncertain Significance variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: PP6 - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 30, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Apogee2
Benign
Hmtvar
Pathogenic
AlphaMissense
Benign
BayesDel_addAF
Benign
T
DEOGEN2
Benign
T
LIST_S2
Benign
T
MutationTaster
Benign
D
PROVEAN
Pathogenic
D
Sift
Benign
D
Sift4G
Uncertain
D
GERP RS
Varity_R
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at