rs796065303

chr11-823739-GC-G

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_020376.4(PNPLA2):c.808del(p.His270ThrfsTer50) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PNPLA2 NM_020376.4 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: -2.91

Genes affected

PNPLA2 (HGNC:30802): (patatin like phospholipase domain containing 2) This gene encodes an enzyme which catalyzes the first step in the hydrolysis of triglycerides in adipose tissue. Mutations in this gene are associated with neutral lipid storage disease with myopathy. [provided by RefSeq, Jul 2010]

(HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 11-823739-GC-G is Pathogenic according to our data. Variant chr11-823739-GC-G is described in ClinVar as [Pathogenic]. Clinvar id is 1873.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PNPLA2	NM_020376.4	c.808del	p.His270ThrfsTer50	frameshift_variant	7/10	ENST00000336615.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PNPLA2	ENST00000336615.9	c.808del	p.His270ThrfsTer50	frameshift_variant	7/10	1	NM_020376.4	P1
	ENST00000532946.1	n.430del		non_coding_transcript_exon_variant	3/3	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 945108 Hom.: 0 Cov.: 47 AF XY: 0.00 AC XY: 0 AN XY: 479484

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Neutral lipid storage myopathy Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Oct 30, 2019	This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.His270Thrfs*50) in the PNPLA2 gene. It is expected to result in an absent or disrupted protein product. This variant has been reported in combination with another PNPLA2 variant in an individual affected with neutral lipid storage disease with myopathy (PMID: 17187067, 23449549, 23232698). ClinVar contains an entry for this variant (Variation ID: 1873). For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in PNPLA2 are known to be pathogenic (PMID: 17187067). -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jan 01, 2007	- -

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

LitVar

Other links and lift over

dbSNP: rs796065303; hg19: chr11-823739;