NM_001128203.2:c.286dupG
Variant names:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_001128203.2(PLAAT3):c.286dupG(p.Ala96GlyfsTer16) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
PLAAT3
NM_001128203.2 frameshift
NM_001128203.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.20
Genes affected
PLAAT3 (HGNC:17825): (phospholipase A and acyltransferase 3) Enables N-acyltransferase activity; phospholipase A1 activity; and phospholipase A2 activity. Involved in N-acylphosphatidylethanolamine metabolic process. Predicted to be located in several cellular components, including lysosome; nuclear envelope; and peroxisome. Predicted to be active in cytoplasm. Biomarker of seminoma. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.415 CDS is truncated, and there are 2 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 11-63590200-G-GC is Pathogenic according to our data. Variant chr11-63590200-G-GC is described in ClinVar as [Pathogenic]. Clinvar id is 2691741.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLAAT3 | NM_001128203.2 | c.286dupG | p.Ala96GlyfsTer16 | frameshift_variant | Exon 4 of 5 | ENST00000415826.3 | NP_001121675.1 | |
PLAAT3 | NM_007069.3 | c.286dupG | p.Ala96GlyfsTer16 | frameshift_variant | Exon 3 of 4 | NP_009000.2 | ||
PLAAT3 | XM_011544741.2 | c.331dupG | p.Ala111GlyfsTer16 | frameshift_variant | Exon 3 of 4 | XP_011543043.1 | ||
LOC105369335 | XR_950179.3 | n.*110_*111insC | downstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Lipodystrophy, familial partial, type 9 Pathogenic:1
Mar 06, 2024
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.