NM_000527.5(LDLR):c.324_325delinsTC (p.Cys109Arg) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Apr 28, 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:: RCV003441821.1

Allele description [Variation Report for NM_000527.5(LDLR):c.324_325delinsTC (p.Cys109Arg)]

NM_000527.5(LDLR):c.324_325delinsTC (p.Cys109Arg)

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.324_325delinsTC (p.Cys109Arg)

HGVS:

NC_000019.10:g.11105230_11105231delinsTC
NG_009060.1:g.20850_20851delinsTC
NM_000527.5:c.324_325delinsTCMANE SELECT
NM_001195798.2:c.324_325delinsTC
NM_001195799.2:c.201_202delinsTC
NM_001195800.2:c.314-2162_314-2161delinsTC
NM_001195803.2:c.314-1335_314-1334delinsTC
NP_000518.1:p.Cys109Arg
NP_001182727.1:p.Cys109Arg
NP_001182728.1:p.Cys68Arg
LRG_274:g.20850_20851delinsTC
NC_000019.9:g.11215906_11215907delinsTC
NM_000527.4:c.324_325delGTinsTC
NM_000527.5:c.324_325delinsTC
c.324_325delinsTC

Protein change:

C109R

Links:

LDLR-LOVD, British Heart Foundation: LDLR_000050; dbSNP: rs879254476

NCBI 1000 Genomes Browser:

rs879254476

Molecular consequence:

NM_001195800.2:c.314-2162_314-2161delinsTC - intron variant - [Sequence Ontology: SO:0001627]
NM_001195803.2:c.314-1335_314-1334delinsTC - intron variant - [Sequence Ontology: SO:0001627]
NM_000527.5:c.324_325delinsTC - missense variant - [Sequence Ontology: SO:0001583]
NM_001195798.2:c.324_325delinsTC - missense variant - [Sequence Ontology: SO:0001583]
NM_001195799.2:c.201_202delinsTC - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004168393	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Apr 28, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004168393

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Apr 28, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV004168393.1

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 2988123, 12459547, 34037665, 11313767, 20145306, 35741760)

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

Last Updated: Oct 20, 2024

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