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NM_000527.5(LDLR):c.2100C>T (p.Asp700=) AND Hypercholesterolemia, familial, 1

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Dec 18, 2023
Review status:
criteria provided, conflicting classifications
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:
RCV001126805.6

Allele description [Variation Report for NM_000527.5(LDLR):c.2100C>T (p.Asp700=)]

NM_000527.5(LDLR):c.2100C>T (p.Asp700=)

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.2100C>T (p.Asp700=)
HGVS:
  • NC_000019.10:g.11120482C>T
  • NG_009060.1:g.36102C>T
  • NM_000527.5:c.2100C>TMANE SELECT
  • NM_001195798.2:c.2100C>T
  • NM_001195799.2:c.1977C>T
  • NM_001195800.2:c.1596C>T
  • NM_001195803.2:c.1606+249C>T
  • NP_000518.1:p.Asp700=
  • NP_001182727.1:p.Asp700=
  • NP_001182728.1:p.Asp659=
  • NP_001182729.1:p.Asp532=
  • LRG_274t1:c.2100C>T
  • LRG_274:g.36102C>T
  • NC_000019.9:g.11231158C>T
  • NC_000019.9:g.11231158C>T
  • NM_000527.4:c.2100C>T
Links:
dbSNP: rs759858813
NCBI 1000 Genomes Browser:
rs759858813
Molecular consequence:
  • NM_001195803.2:c.1606+249C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000527.5:c.2100C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195798.2:c.2100C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195799.2:c.1977C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195800.2:c.1596C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
2

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
SCV001286050Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Uncertain significance
(Apr 28, 2017) 		germlineclinical testing

Citation Link,

SCV004818498All of Us Research Program, National Institutes of Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely Benign
(Dec 18, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown2not providednot provided108544not providedclinical testing

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 Illumina Laboratory Services, Illumina, SCV001286050.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

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

From All of Us Research Program, National Institutes of Health, SCV004818498.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown108544not providednot provided2not providednot providednot provided

Last Updated: Sep 29, 2024