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NM_000527.5(LDLR):c.932_939delinsGAGAGTGG (p.Lys311_Cys313delinsArgGluTrp) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 3, 2023
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:
RCV000519981.3

Allele description [Variation Report for NM_000527.5(LDLR):c.932_939delinsGAGAGTGG (p.Lys311_Cys313delinsArgGluTrp)]

NM_000527.5(LDLR):c.932_939delinsGAGAGTGG (p.Lys311_Cys313delinsArgGluTrp)

Gene:
LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_000527.5(LDLR):c.932_939delinsGAGAGTGG (p.Lys311_Cys313delinsArgGluTrp)
HGVS:
  • NC_000019.10:g.11107506_11107513delinsGAGAGTGG
  • NG_009060.1:g.23126_23133delinsGAGAGTGG
  • NM_000527.5:c.932_939delinsGAGAGTGGMANE SELECT
  • NM_001195798.2:c.932_939delinsGAGAGTGG
  • NM_001195799.2:c.809_816delinsGAGAGTGG
  • NM_001195800.2:c.428_435delinsGAGAGTGG
  • NM_001195803.2:c.551_558delinsGAGAGTGG
  • NP_000518.1:p.Lys311_Cys313delinsArgGluTrp
  • NP_000518.1:p.Lys311_Cys313delinsArgGluTrp
  • NP_001182727.1:p.Lys311_Cys313delinsArgGluTrp
  • NP_001182728.1:p.Lys270_Cys272delinsArgGluTrp
  • NP_001182729.1:p.Lys143_Cys145delinsArgGluTrp
  • NP_001182732.1:p.Lys184_Cys186delinsArgGluTrp
  • LRG_274t1:c.932_939delinsGAGAGTGG
  • LRG_274:g.23126_23133delinsGAGAGTGG
  • LRG_274p1:p.Lys311_Cys313delinsArgGluTrp
  • NC_000019.9:g.11218182_11218189delinsGAGAGTGG
  • NM_000527.4:c.932_939delAAGAGTGCinsGAGAGTGG
  • NM_000527.4:c.932_939delinsGAGAGTGG
Links:
dbSNP: rs1555803913
NCBI 1000 Genomes Browser:
rs1555803913
Molecular consequence:
  • NM_000527.5:c.932_939delinsGAGAGTGG - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195798.2:c.932_939delinsGAGAGTGG - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195799.2:c.809_816delinsGAGAGTGG - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195800.2:c.428_435delinsGAGAGTGG - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195803.2:c.551_558delinsGAGAGTGG - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000622070GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(Apr 3, 2023) 		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, SCV000622070.4

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

Description

The K311R and C313W variants (also reported as K290R/C292W due to alternate nomenclature) always occur in combination and have been reported in many individuals from different ethnic backgrounds with FH (Van Leuven et al., 2001; Descamps et al., 2001; Fouchier et al., 2005; van der Graaf et al., 2011); Not observed at significant frequency in large population cohorts (gnomAD); The C313 residue participates in disulfide bonding with another cysteine residue which is critical for correct protein structure, and is located in the LDL-receptor class A7 repeat domain which is necessary for ligand binding (Sudhof et al., 1985; Rudenko et al., 2002); In silico analysis supports a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 21382890, 11257257, 11737238, 12436241, 16250003, 20506408)

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

Last Updated: Apr 15, 2023