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NM_000527.5(LDLR):c.1765G>C (p.Asp589His) AND Hypercholesterolemia, familial, 1

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Aug 29, 2022
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV002505198.2

Allele description

NM_000527.5(LDLR):c.1765G>C (p.Asp589His)

Gene:
LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_000527.5(LDLR):c.1765G>C (p.Asp589His)
Other names:
NM_000527.5(LDLR):c.1765G>C; p.Asp589His
HGVS:
  • NC_000019.10:g.11116918G>C
  • NG_009060.1:g.32538G>C
  • NM_000527.5:c.1765G>CMANE SELECT
  • NM_001195798.2:c.1765G>C
  • NM_001195799.2:c.1642G>C
  • NM_001195800.2:c.1261G>C
  • NM_001195803.2:c.1384G>C
  • NP_000518.1:p.Asp589His
  • NP_000518.1:p.Asp589His
  • NP_001182727.1:p.Asp589His
  • NP_001182728.1:p.Asp548His
  • NP_001182729.1:p.Asp421His
  • NP_001182732.1:p.Asp462His
  • LRG_274t1:c.1765G>C
  • LRG_274:g.32538G>C
  • LRG_274p1:p.Asp589His
  • NC_000019.9:g.11227594G>C
  • NM_000527.4:c.1765G>C
Protein change:
D421H
Links:
dbSNP: rs201971888
NCBI 1000 Genomes Browser:
rs201971888
Molecular consequence:
  • NM_000527.5:c.1765G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195798.2:c.1765G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195799.2:c.1642G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195800.2:c.1261G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195803.2:c.1384G>C - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
no known functional consequence - Comment(s)

Condition(s)

Name:
Hypercholesterolemia, familial, 1
Synonyms:
LDL RECEPTOR DISORDER; Hyperlipoproteinemia Type IIa; HYPER-LOW-DENSITY-LIPOPROTEINEMIA; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007750; MedGen: C0745103; Orphanet: 391665; OMIM: 143890

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002817144ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel
reviewed by expert panel

(ClinGen FH ACMG Specifications v1-2)		Uncertain significance
(Aug 29, 2022) 		germlinecuration

Citation Link,

SCV004807976Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 29, 2024) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel, SCV002817144.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The NM_000527.5(LDLR):c.1765G>C (p.Asp589His) variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes PM2 and BP4 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: PM2 - PopMax MAF = 0.000008790 (0.0009%) in Non-Finnish European exomes+genomes (gnomAD v2.1.1) BP4 - REVEL = 0.424. It is below 0.5, splicing evaluation needed. Functional data on splicing not available. A) variant not on limits. B) does not create AG or GT Variant is not predicted to alter splicing

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

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004807976.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 7, 2024