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NM_002335.4(LRP5):c.1058G>A (p.Arg353Gln) AND Osteoporosis with pseudoglioma

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 24, 2021
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:
RCV001728176.1

Allele description [Variation Report for NM_002335.4(LRP5):c.1058G>A (p.Arg353Gln)]

NM_002335.4(LRP5):c.1058G>A (p.Arg353Gln)

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.1058G>A (p.Arg353Gln)
HGVS:
  • NC_000011.10:g.68386358G>A
  • NG_015835.2:g.78719G>A
  • NM_001291902.2:c.-708G>A
  • NM_002335.4:c.1058G>AMANE SELECT
  • NP_002326.2:p.Arg353Gln
  • NC_000011.9:g.68153826G>A
Protein change:
R353Q
Links:
dbSNP: rs2153153067
NCBI 1000 Genomes Browser:
rs2153153067
Molecular consequence:
  • NM_001291902.2:c.-708G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_002335.4:c.1058G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001976614Breda Genetics srl
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jun 24, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineno1not providednot providednot providednot providedclinical 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 Breda Genetics srl, SCV001976614.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)

Description

The variant c.1058G>A (p.Arg353Gln) is reported as pathogenic in the Global Variome shared LOVD v.3.0 database. The variant is not reported in the dbSNP, gnomAD, or ClinVar databases. The nucleotide position is moderately conserved across 35 mammalian species (GERP RS: 3.81). In silico analysis mostly indicates that the variant might be damaging. This variant has been reported in homozygosity by Ai et al. (2005), in a patient with blindness (6 years) and osteoporosis with onset at 20 years (PMID: 16252235), and by Tang et al. (2017) in compound heterozygosity to a splice variant, in a patient with congenital blindness, but without skeletal features (PMID: 29181528).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot provided1not providednot providednot provided

Last Updated: Sep 29, 2024