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NM_015627.3(LDLRAP1):c.429C>A (p.Cys143Ter) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 17, 2018
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:
RCV000760903.1

Allele description [Variation Report for NM_015627.3(LDLRAP1):c.429C>A (p.Cys143Ter)]

NM_015627.3(LDLRAP1):c.429C>A (p.Cys143Ter)

Gene:
LDLRAP1:low density lipoprotein receptor adaptor protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.11
Genomic location:
Preferred name:
NM_015627.3(LDLRAP1):c.429C>A (p.Cys143Ter)
HGVS:
  • NC_000001.11:g.25557237C>A
  • NG_008932.1:g.18653C>A
  • NM_015627.3:c.429C>AMANE SELECT
  • NP_056442.2:p.Cys143Ter
  • NP_056442.2:p.Cys143Ter
  • LRG_276t1:c.429C>A
  • LRG_276:g.18653C>A
  • LRG_276p1:p.Cys143Ter
  • NC_000001.10:g.25883728C>A
  • NM_015627.2:c.429C>A
Protein change:
C143*
Links:
dbSNP: rs777648532
NCBI 1000 Genomes Browser:
rs777648532
Molecular consequence:
  • NM_015627.3:c.429C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000890799GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Dec 17, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000890799.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The C143X variant in the LDLRAP1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The C143X variant is not observed in large population cohorts (Lek et al., 2016). We interpret C143X as a pathogenic variant.

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

Last Updated: Apr 23, 2022