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

Recent activity

Clear Turn Off Turn On

Homo sapiens ATPase H+ transporting V0 subunit d1 (ATP6V0D1), RefSeqGene on chro...
Homo sapiens ATPase H+ transporting V0 subunit d1 (ATP6V0D1), RefSeqGene on chromosome 16
gi|224809278|ref|NG_011482.1|

Nucleotide
1131516[uid] (1)
Taxonomy
Taraxacum tanylepis (0)
Conserved Domains
Mus musculus ribosomal protein S6 kinase, polypeptide 2 (Rps6kb2), transcript va...
Mus musculus ribosomal protein S6 kinase, polypeptide 2 (Rps6kb2), transcript variant 3, non-coding RNA
gi|1340723194|ref|NR_153661.1|

Nucleotide
AAK83644 (0)
GEO DataSets

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000622070	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 3, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000622070

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Apr 3, 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, SCV000622070.4

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

#	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: Apr 15, 2023

ClinVar

Relating variation to medicine