Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000527.5(LDLR):c.346T>C (p.Cys116Arg)

Help
Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Aug 29, 2018)
Last evaluated:
Mar 13, 2018
Accession:
VCV000251163.1
Variation ID:
251163
Description:
single nucleotide variant
Help

NM_000527.5(LDLR):c.346T>C (p.Cys116Arg)

Allele ID
245501
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.2
Genomic location
19: 11105252 (GRCh38) GRCh38 UCSC
19: 11215928 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001195803.2:c.314-1313T>C
NM_001195800.2:c.314-2140T>C
NM_000527.4:c.346T>C NP_000518.1:p.Cys116Arg missense
... more HGVS
Protein change
C116R, C75R
Other names
FH Alghero
Canonical SPDI
NC_000019.10:11105251:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA10584862
LDLR-LOVD, British Heart Foundation: LDLR_000360
UniProtKB: P01130#VAR_005317
dbSNP: rs879254482
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Mar 13, 2018 RCV000237774.3
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LDLR Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
3087 3287

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Mar 25, 2016)
criteria provided, single submitter
Method: literature only
Familial hypercholesterolemia
(Autosomal dominant inheritance)
Allele origin: germline
LDLR-LOVD, British Heart Foundation
Accession: SCV000294642.2
Submitted: (Apr 20, 2016)
Evidence details
Publications
PubMed (2)
Pathogenic
(Mar 01, 2016)
criteria provided, single submitter
Method: research
Familial hypercholesterolemia
(Autosomal dominant inheritance)
Allele origin: germline
Fundacion Hipercolesterolemia Familiar
Study: SAFEHEART
Accession: SCV000607450.1
Submitted: (Apr 20, 2017)
Evidence details
Pathogenic
(Mar 13, 2018)
criteria provided, single submitter
Method: clinical testing
Familial hypercholesterolemia
Allele origin: germline
Invitae
Accession: SCV000816330.1
Submitted: (Aug 29, 2018)
Evidence details
Publications
PubMed (6)
Comment:
This sequence change replaces cysteine with arginine at codon 116 of the LDLR protein (p.Cys116Arg). The cysteine residue is highly conserved and there is a … (more)

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Activity-associated effect of LDL receptor missense variants located in the cysteine-rich repeats. Etxebarria A Atherosclerosis 2015 PMID: 25545329
Update and analysis of the University College London low density lipoprotein receptor familial hypercholesterolemia database. Leigh SE Annals of human genetics 2008 PMID: 18325082
Molecular genetics of familial hypercholesterolemia in Spain: Ten novel LDLR mutations and population analysis. García-García AB Human mutation 2001 PMID: 11668640
Influence of beta(0)-thalassemia on the phenotypic expression of heterozygous familial hypercholesterolemia : a study of patients with familial hypercholesterolemia from Sardinia. Deiana L Arteriosclerosis, thrombosis, and vascular biology 2000 PMID: 10634824
Identification of recurrent and novel mutations in the LDL receptor gene in Spanish patients with familial hypercholesterolemia. Mutations in brief no. 135. Online. Cenarro A Human mutation 1998 PMID: 10206683
The solution structure of human epidermal growth factor. Cooke RM Nature 1987 PMID: 3495735
Epidermal growth factor. Location of disulfide bonds. Savage CR Jr The Journal of biological chemistry 1973 PMID: 4750422

Text-mined citations for rs879254482...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 29, 2020