11-63590200-G-GC

Position:

• chr11-63590200-G-GC

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

The NM_001128203.2(PLAAT3):​c.286_287insG​(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
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• 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]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• 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/exons	MANE	UniProt
PLAAT3	NM_001128203.2	c.286_287insG	p.Ala96GlyfsTer16	frameshift_variant	4/5	ENST00000415826.3
PLAAT3	NM_007069.3	c.286_287insG	p.Ala96GlyfsTer16	frameshift_variant	3/4
PLAAT3	XM_011544741.2	c.331_332insG	p.Ala111GlyfsTer16	frameshift_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLAAT3	ENST00000415826.3	c.286_287insG	p.Ala96GlyfsTer16	frameshift_variant	4/5	2	NM_001128203.2	P1
PLAAT3	ENST00000323646.9	c.286_287insG	p.Ala96GlyfsTer16	frameshift_variant	3/4	1		P1
PLAAT3	ENST00000394613.3	n.380_381insG		non_coding_transcript_exon_variant	3/4	1

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

Submissions by phenotype

Lipodystrophy, familial partial, type 9 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 06, 2024

- -

Computational scores

Source: dbNSFP v4.3

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;