chr16-28878787-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_004320.6(ATP2A1):āc.116A>Gā(p.Asn39Ser) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,638 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004320.6 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2A1 | NM_004320.6 | c.116A>G | p.Asn39Ser | missense_variant, splice_region_variant | 1/23 | ENST00000395503.9 | |
ATP2A1 | NM_173201.5 | c.116A>G | p.Asn39Ser | missense_variant, splice_region_variant | 1/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2A1 | ENST00000395503.9 | c.116A>G | p.Asn39Ser | missense_variant, splice_region_variant | 1/23 | 1 | NM_004320.6 | P4 | |
ATP2A1-AS1 | ENST00000691192.2 | n.1150T>C | non_coding_transcript_exon_variant | 1/1 | |||||
ATP2A1 | ENST00000357084.7 | c.116A>G | p.Asn39Ser | missense_variant, splice_region_variant | 1/22 | 2 | A1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461638Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727136
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Brody myopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 25, 2021 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with ATP2A1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 39 of the ATP2A1 protein (p.Asn39Ser). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.