rs1555515558
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PP5_Moderate
The NM_004320.6(ATP2A1):c.909_920delinsACGGCATA(p.Val304ArgfsTer29) variant causes a frameshift change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
ATP2A1
NM_004320.6 frameshift
NM_004320.6 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 10.0
Genes affected
ATP2A1 (HGNC:811): (ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1) This gene encodes one of the SERCA Ca(2+)-ATPases, which are intracellular pumps located in the sarcoplasmic or endoplasmic reticula of muscle cells. This enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen, and is involved in muscular excitation and contraction. Mutations in this gene cause some autosomal recessive forms of Brody disease, characterized by increasing impairment of muscular relaxation during exercise. Alternative splicing results in three transcript variants encoding different isoforms. [provided by RefSeq, Oct 2013]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PP5
?
Variant 16-28887703-TGTGGCTGCCAT-ACGGCATA is Pathogenic according to our data. Variant chr16-28887703-TGTGGCTGCCAT-ACGGCATA is described in ClinVar as [Pathogenic]. Clinvar id is 464091.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2A1 | NM_004320.6 | c.909_920delinsACGGCATA | p.Val304ArgfsTer29 | frameshift_variant | 8/23 | ENST00000395503.9 | |
ATP2A1 | NM_001286075.2 | c.534_545delinsACGGCATA | p.Val179ArgfsTer29 | frameshift_variant | 6/21 | ||
ATP2A1 | NM_173201.5 | c.909_920delinsACGGCATA | p.Val304ArgfsTer29 | frameshift_variant | 8/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2A1 | ENST00000395503.9 | c.909_920delinsACGGCATA | p.Val304ArgfsTer29 | frameshift_variant | 8/23 | 1 | NM_004320.6 | P4 | |
ATP2A1 | ENST00000357084.7 | c.909_920delinsACGGCATA | p.Val304ArgfsTer29 | frameshift_variant | 8/22 | 2 | A1 | ||
ATP2A1 | ENST00000536376.5 | c.534_545delinsACGGCATA | p.Val179ArgfsTer29 | frameshift_variant | 6/21 | 2 | |||
ATP2A1 | ENST00000564732.1 | c.41_52delinsACGGCATA | p.Val15ArgfsTer29 | frameshift_variant, NMD_transcript_variant | 1/7 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Brody myopathy Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Feb 25, 2021 | This sequence change creates a premature translational stop signal (p.Val304Argfs*29) in the ATP2A1 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with ATP2A1-related disease. Loss-of-function variants in ATP2A1 are known to be pathogenic (PMID: 8841193). For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at