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NM_000527.5(LDLR):c.190+4_190+7del AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 29, 2022
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:
RCV002223071.1

Allele description [Variation Report for NM_000527.5(LDLR):c.190+4_190+7del]

NM_000527.5(LDLR):c.190+4_190+7del

Gene:
LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_000527.5(LDLR):c.190+4_190+7del
HGVS:
  • NC_000019.10:g.11100349_11100352del
  • NG_009060.1:g.15969_15972del
  • NM_000527.5:c.190+4_190+7delMANE SELECT
  • NM_001195798.2:c.190+4_190+7del
  • NM_001195799.2:c.190+4_190+7del
  • NM_001195800.2:c.190+4_190+7del
  • NM_001195803.2:c.190+4_190+7del
  • LRG_274t1:c.190+4_190+7del
  • LRG_274:g.15969_15972del
  • NC_000019.9:g.11211025_11211028del
  • NM_000527.4:c.190+4_190+7delAGTC
Links:
dbSNP: rs2147210820
NCBI 1000 Genomes Browser:
rs2147210820
Molecular consequence:
  • NM_000527.5:c.190+4_190+7del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195798.2:c.190+4_190+7del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195799.2:c.190+4_190+7del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195800.2:c.190+4_190+7del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195803.2:c.190+4_190+7del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002500742Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Mar 29, 2022) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

FH ALERT: efficacy of a novel approach to identify patients with familial hypercholesterolemia.

Fath F, Bengeser A, Barresi M, Binner P, Schwab S, Ray KK, Krämer BK, Fraass U, März W.

Sci Rep. 2021 Oct 14;11(1):20421. doi: 10.1038/s41598-021-99961-y.

PubMed [citation]
PMID:
34650182
PMCID:
PMC8516913

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002500742.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: LDLR c.190+4_190+7delAGTC alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 250582 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.190+4_190+7delAGTC has been reported in the literature in individuals affected with Hypercholesterolemia (Fath_2021). However, this report does not provide unequivocal conclusions about association of the variant with Familial Hypercholesterolemia. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Sep 29, 2024