NM_002335.4(LRP5):c.1512G>A (p.Trp504Ter) AND Osteoporosis with pseudoglioma

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 22, 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:: RCV002052059.1

Allele description [Variation Report for NM_002335.4(LRP5):c.1512G>A (p.Trp504Ter)]

NM_002335.4(LRP5):c.1512G>A (p.Trp504Ter)

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.1512G>A (p.Trp504Ter)

HGVS:

NC_000011.10:g.68389980G>A
NG_015835.2:g.82341G>A
NM_001291902.2:c.-354+3268G>A
NM_002335.4:c.1512G>AMANE SELECT
NP_002326.2:p.Trp504Ter
NC_000011.9:g.68157448G>A

Protein change:

W504*

Links:

dbSNP: rs545508982

NCBI 1000 Genomes Browser:

rs545508982

Molecular consequence:

NM_001291902.2:c.-354+3268G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_002335.4:c.1512G>A - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Name:: Osteoporosis with pseudoglioma (OPPG)
Synonyms:: Osteogenesis imperfecta ocular form; Pseudoglioma with bone fragility
Identifiers:: MONDO: MONDO:0009820; MedGen: C0432252; Orphanet: 2788; OMIM: 259770

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002318470	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 22, 2022)	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

SCV002318470

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 22, 2022)

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	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From 3billion, SCV002318470.1

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

Description

Stop-gained (nonsense): predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000004). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Dec 24, 2023

ClinVar

Relating variation to medicine