NM_002334.4(LRP4):c.5678_5682del (p.Trp1893fs) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 22, 2024
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:: RCV003790483.2

Allele description [Variation Report for NM_002334.4(LRP4):c.5678_5682del (p.Trp1893fs)]

NM_002334.4(LRP4):c.5678_5682del (p.Trp1893fs)

Genes:

LRP4:LDL receptor related protein 4 [Gene - OMIM - HGNC]
LRP4-AS1:LRP4 antisense RNA 1 [Gene - HGNC]

Variant type:

Deletion

Cytogenetic location:

11p11.2

Genomic location:

Preferred name:

NM_002334.4(LRP4):c.5678_5682del (p.Trp1893fs)

HGVS:

NC_000011.10:g.46859019_46859023del
NG_021394.1:g.64600_64604del
NG_021394.2:g.64527_64531del
NM_002334.4:c.5678_5682delMANE SELECT
NP_002325.2:p.Trp1893fs
NC_000011.9:g.46880570_46880574del

Protein change:

W1893fs

Molecular consequence:

NM_002334.4:c.5678_5682del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Cenani-Lenz syndactyly syndrome
Synonyms:: SYNDACTYLY, TYPE VII; Syndactyly Cenani Lenz type; Cenani syndactylism; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008931; MedGen: C1859309; Orphanet: 3258; OMIM: 212780

Name:: Sclerosteosis 2 (SOST2)
Identifiers:: MONDO: MONDO:0013679; MedGen: C3280402; Orphanet: 3152; OMIM: 614305

Name:: Congenital myasthenic syndrome 17
Identifiers:: MONDO: MONDO:0014578; MedGen: C4225377; Orphanet: 590; OMIM: 616304

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004580361	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 22, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004580361

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 22, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

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, SCV004580361.1

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

Description

This sequence change creates a premature translational stop signal (p.Trp1893Serfs*2) in the LRP4 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 13 amino acid(s) of the LRP4 protein. This variant is present in population databases (rs747021035, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with LRP4-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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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