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NC_000019.9:g.(?_11233830)_(11241992_?)del AND Familial hypercholesterolemia

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 6, 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:
RCV004581015.2

Allele description [Variation Report for NC_000019.9:g.(?_11233830)_(11241992_?)del]

NC_000019.9:g.(?_11233830)_(11241992_?)del

Gene:
LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
19p13.2
Genomic location:
Chr19: 11233830 - 11241992 (on Assembly GRCh37)
Preferred name:
NC_000019.9:g.(?_11233830)_(11241992_?)del
HGVS:
NC_000019.9:g.(?_11233830)_(11241992_?)del

Condition(s)

Name:
Familial hypercholesterolemia
Identifiers:
MONDO: MONDO:0005439; MedGen: C0020445; OMIM: PS143890

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005063558Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 6, 2023) 		unknownclinical testing

PubMed (12)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Characterization of deletions in the LDL receptor gene in patients with familial hypercholesterolemia in the United Kingdom.

Sun XM, Webb JC, Gudnason V, Humphries S, Seed M, Thompson GR, Knight BL, Soutar AK.

Arterioscler Thromb. 1992 Jul;12(7):762-70.

PubMed [citation]
PMID:
1319734

Update of the molecular basis of familial hypercholesterolemia in The Netherlands.

Fouchier SW, Kastelein JJ, Defesche JC.

Hum Mutat. 2005 Dec;26(6):550-6.

PubMed [citation]
PMID:
16250003
See all PubMed Citations (12)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005063558.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (12)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 15-18 of the LDLR gene, which includes the termination codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. While this deletion is not anticipated to lead to nonsense mediated decay, it is expected to alter mRNA translation or result in a truncated protein product. A similar copy number variant has been observed in individuals with hypercholesterolemia (PMID: 1319734, 16250003, 17142622, 24075752; Invitae). This variant disrupts the p.Val797 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 7649549, 9763532, 19446849, 20145306, 22698793, 22859806, 23375686). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024