NM_002335.4(LRP5):c.4517C>T (p.Thr1506Met) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 14, 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:: RCV001238713.7

Allele description [Variation Report for NM_002335.4(LRP5):c.4517C>T (p.Thr1506Met)]

NM_002335.4(LRP5):c.4517C>T (p.Thr1506Met)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.2

Genomic location:

Preferred name:

NM_002335.4(LRP5):c.4517C>T (p.Thr1506Met)

HGVS:

NC_000011.10:g.68446464C>T
NG_015835.2:g.138825C>T
NM_001291902.2:c.2774C>T
NM_002335.4:c.4517C>TMANE SELECT
NP_001278831.1:p.Thr925Met
NP_002326.2:p.Thr1506Met
NC_000011.9:g.68213932C>T
NG_015835.1:g.138825C>T
NM_002335.3:c.4517C>T

Protein change:

T1506M

Links:

dbSNP: rs371173423

NCBI 1000 Genomes Browser:

rs371173423

Molecular consequence:

NM_001291902.2:c.2774C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002335.4:c.4517C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001411541	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 14, 2024)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 25711638, 30452590, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001411541

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 14, 2024)

germline

clinical testing

PubMed (3)
[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

Next-generation sequencing and novel variant determination in a cohort of 92 familial exudative vitreoretinopathy patients.

Salvo J, Lyubasyuk V, Xu M, Wang H, Wang F, Nguyen D, Wang K, Luo H, Wen C, Shi C, Lin D, Zhang K, Chen R.

Invest Ophthalmol Vis Sci. 2015 Feb 24;56(3):1937-46. doi: 10.1167/iovs.14-16065.

PubMed [citation]

PMID:: 25711638
PMCID:: PMC4365990

Spectrum of Variants in 389 Chinese Probands With Familial Exudative Vitreoretinopathy.

Li JK, Li Y, Zhang X, Chen CL, Rao YQ, Fei P, Zhang Q, Zhao P, Li J.

Invest Ophthalmol Vis Sci. 2018 Nov 1;59(13):5368-5381. doi: 10.1167/iovs.17-23541.

PubMed [citation]

PMID:: 30452590

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001411541.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 1506 of the LRP5 protein (p.Thr1506Met). This variant is present in population databases (rs371173423, gnomAD 0.006%). This missense change has been observed in individual(s) with familial exudative vitreoretinopathy (PMID: 25711638, 30452590). ClinVar contains an entry for this variant (Variation ID: 964485). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt LRP5 protein function with a negative predictive value of 95%. 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: Feb 20, 2024

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