NC_000019.10:g.(?_11100213)_(11107528_?)del AND Familial hypercholesterolemia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 13, 2021
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:: RCV000805901.7

Allele description [Variation Report for NC_000019.10:g.(?_11100213)_(11107528_?)del]

NC_000019.10:g.(?_11100213)_(11107528_?)del

Gene:

LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NC_000019.10:g.(?_11100213)_(11107528_?)del

HGVS:

NC_000019.10:g.(?_11100213)_(11107528_?)del
NC_000019.9:g.(?_11210889)_(11218204_?)del

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000945876	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 13, 2021)	germline	clinical testing	PubMed (10) [See all records that cite these PMIDs] 1319734, 2837085, 22883975, 12837857, 15823276, 16343504, 21376320, 25962062, 27765764, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000945876

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 13, 2021)

germline

clinical testing

PubMed (10)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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

Characterization of six partial deletions in the low-density-lipoprotein (LDL) receptor gene causing familial hypercholesterolemia (FH).

Langlois S, Kastelein JJ, Hayden MR.

Am J Hum Genet. 1988 Jul;43(1):60-8.

PubMed [citation]

PMID:: 2837085
PMCID:: PMC1715276

See all PubMed Citations (10)

Details of each submission

From Invitae, SCV000945876.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (10)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 2-6 of the LDLR gene. This variant would be expected to be in-frame, preserving the integrity of the reading frame. A similar copy number variant has been observed in individuals with familial hypercholesterolemia (PMID: 1319734, 2837085, 22883975). This variant disrupts the p.Asp90 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 12837857, 15823276, 16343504, 21376320, 25962062, 27765764). 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 11, 2023

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