NM_002335.4(LRP5):c.1990AAC[1] (p.Asn665del) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 18, 2023
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:: RCV001203297.8

Allele description [Variation Report for NM_002335.4(LRP5):c.1990AAC[1] (p.Asn665del)]

NM_002335.4(LRP5):c.1990AAC[1] (p.Asn665del)

Gene:

LRP5:LDL receptor related protein 5 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

11q13.2

Genomic location:

Preferred name:

NM_002335.4(LRP5):c.1990AAC[1] (p.Asn665del)

HGVS:

NC_000011.10:g.68406712AAC[1]
NG_015835.2:g.99073AAC[1]
NM_001291902.2:c.247AAC[1]
NM_002335.4:c.1990AAC[1]MANE SELECT
NP_001278831.1:p.Asn84del
NP_002326.2:p.Asn665del
NC_000011.9:g.68174180AAC[1]
NC_000011.9:g.68174180_68174182del
NG_015835.1:g.99073AAC[1]
NM_002335.3:c.1993_1995del
NM_002335.4:c.1993_1995delMANE SELECT

Protein change:

N665del

Links:

dbSNP: rs780882911

NCBI 1000 Genomes Browser:

rs780882911

Molecular consequence:

NM_001291902.2:c.247AAC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_002335.4:c.1990AAC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001374454	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 18, 2023)	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

SCV001374454

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 18, 2023)

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, SCV001374454.5

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

Description

This variant, c.1993_1995del, results in the deletion of 1 amino acid(s) of the LRP5 protein (p.Asn665del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs780882911, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with LRP5-related conditions. ClinVar contains an entry for this variant (Variation ID: 934824). 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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