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NM_004525.3(LRP2):c.13753C>T (p.Arg4585Ter) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 1, 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:
RCV001861449.2

Allele description [Variation Report for NM_004525.3(LRP2):c.13753C>T (p.Arg4585Ter)]

NM_004525.3(LRP2):c.13753C>T (p.Arg4585Ter)

Gene:
LRP2:LDL receptor related protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q31.1
Genomic location:
Preferred name:
NM_004525.3(LRP2):c.13753C>T (p.Arg4585Ter)
HGVS:
  • NC_000002.12:g.169129060G>A
  • NG_012634.1:g.238553C>T
  • NM_004525.3:c.13753C>TMANE SELECT
  • NP_004516.2:p.Arg4585Ter
  • LRG_1300t1:c.13753C>T
  • LRG_1300:g.238553C>T
  • LRG_1300p1:p.Arg4585Ter
  • NC_000002.11:g.169985570G>A
  • NM_004525.2:c.13753C>T
Protein change:
R4585*
Links:
dbSNP: rs202057289
NCBI 1000 Genomes Browser:
rs202057289
Molecular consequence:
  • NM_004525.3:c.13753C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002228845Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Nov 1, 2022)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutations in LRP2, which encodes the multiligand receptor megalin, cause Donnai-Barrow and facio-oculo-acoustico-renal syndromes.

Kantarci S, Al-Gazali L, Hill RS, Donnai D, Black GC, Bieth E, Chassaing N, Lacombe D, Devriendt K, Teebi A, Loscertales M, Robson C, Liu T, MacLaughlin DT, Noonan KM, Russell MK, Walsh CA, Donahoe PK, Pober BR.

Nat Genet. 2007 Aug;39(8):957-9. Epub 2007 Jul 15.

PubMed [citation]
PMID:
17632512
PMCID:
PMC2891728

Variable expression pattern in Donnai-Barrow syndrome: Report of two novel LRP2 mutations and review of the literature.

Khalifa O, Al-Sahlawi Z, Imtiaz F, Ramzan K, Allam R, Al-Mostafa A, Abdel-Fattah M, Abuharb G, Nester M, Verloes A, Al-Zaidan H.

Eur J Med Genet. 2015 May;58(5):293-9. doi: 10.1016/j.ejmg.2014.12.008. Epub 2015 Feb 13. Review.

PubMed [citation]
PMID:
25682901
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002228845.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Arg4585*) in the LRP2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LRP2 are known to be pathogenic (PMID: 17632512, 25682901). This variant is present in population databases (rs202057289, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with LRP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 374076). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 7, 2023