NM_020376.4(PNPLA2):c.440del (p.Phe147fs) AND Neutral lipid storage myopathy

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 16, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001941995.4

Allele description [Variation Report for NM_020376.4(PNPLA2):c.440del (p.Phe147fs)]

NM_020376.4(PNPLA2):c.440del (p.Phe147fs)

Gene:

PNPLA2:patatin like phospholipase domain containing 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11p15.5

Genomic location:

Preferred name:

NM_020376.4(PNPLA2):c.440del (p.Phe147fs)

HGVS:

NC_000011.10:g.821977del
NG_023394.1:g.8077del
NM_020376.4:c.440delMANE SELECT
NP_065109.1:p.Phe147fs
NC_000011.9:g.821975del
NC_000011.9:g.821977del

Protein change:

F147fs

Links:

dbSNP: rs2133847468

NCBI 1000 Genomes Browser:

rs2133847468

Molecular consequence:

NM_020376.4:c.440del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Neutral lipid storage myopathy (NLSDM)
Synonyms:: Neutral lipid storage disease with myopathy; Neutral lipid storage disease without ichthyosis
Identifiers:: MONDO: MONDO:0012545; MedGen: C1853136; Orphanet: 98908; OMIM: 610717

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Urochloa brizantha
Urochloa brizantha
Urochloa brizantha

BioProject
CDK5 cyclin dependent kinase 5 [Homo sapiens]
CDK5 cyclin dependent kinase 5 [Homo sapiens]
Gene ID:1020

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002235057	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 16, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 17187067, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002235057

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 16, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The gene encoding adipose triglyceride lipase (PNPLA2) is mutated in neutral lipid storage disease with myopathy.

Fischer J, Lefèvre C, Morava E, Mussini JM, Laforêt P, Negre-Salvayre A, Lathrop M, Salvayre R.

Nat Genet. 2007 Jan;39(1):28-30. Epub 2006 Dec 24.

PubMed [citation]

PMID:: 17187067

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002235057.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Phe147Serfs*109) in the PNPLA2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PNPLA2 are known to be pathogenic (PMID: 17187067). This variant has not been reported in the literature in individuals affected with PNPLA2-related conditions. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1454689).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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