NM_001128203.2:c.286dupG

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

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 7.20
Variant links:
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
PLAAT3NM_001128203.2 linkc.286dupG p.Ala96GlyfsTer16 frameshift_variant Exon 4 of 5 ENST00000415826.3 NP_001121675.1 P53816A0A024R561
PLAAT3NM_007069.3 linkc.286dupG p.Ala96GlyfsTer16 frameshift_variant Exon 3 of 4 NP_009000.2 P53816A0A024R561
PLAAT3XM_011544741.2 linkc.331dupG p.Ala111GlyfsTer16 frameshift_variant Exon 3 of 4 XP_011543043.1
LOC105369335XR_950179.3 linkn.*110_*111insC downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PLAAT3ENST00000415826.3 linkc.286dupG p.Ala96GlyfsTer16 frameshift_variant Exon 4 of 5 2 NM_001128203.2 ENSP00000389124.1 P53816

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-63357672; API