NC_000001.10:g.(?_25870180)_(26795632_?)del AND Hypercholesterolemia, familial, 4

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 14, 2020
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:: RCV001385284.4

Allele description

NC_000001.10:g.(?_25870180)_(26795632_?)del

Genes:

CD52:CD52 molecule [Gene - OMIM - HGNC]
PDIK1L:PDLIM1 interacting kinase 1 like [Gene - OMIM - HGNC]
SH3BGRL3:SH3 domain binding glutamate rich protein like 3 [Gene - OMIM - HGNC]
UBXN11:UBX domain protein 11 [Gene - OMIM - HGNC]
AUNIP:aurora kinase A and ninein interacting protein [Gene - OMIM - HGNC]
CATSPER4:cation channel sperm associated 4 [Gene - OMIM - HGNC]
CEP85:centrosomal protein 85 [Gene - OMIM - HGNC]
CNKSR1:connector enhancer of kinase suppressor of Ras 1 [Gene - OMIM - HGNC]
CRYBG2:crystallin beta-gamma domain containing 2 [Gene - OMIM - HGNC]
DHDDS:dehydrodolichyl diphosphate synthase subunit [Gene - OMIM - HGNC]
EXTL1:exostosin like glycosyltransferase 1 [Gene - OMIM - HGNC]
FAM110D:family with sequence similarity 110 member D [Gene - HGNC]
LIN28A:lin-28 homolog A [Gene - OMIM - HGNC]
LDLRAP1:low density lipoprotein receptor adaptor protein 1 [Gene - OMIM - HGNC]
MAN1C1:mannosidase alpha class 1C member 1 [Gene - OMIM - HGNC]
MTFR1L:mitochondrial fission regulator 1 like [Gene - HGNC]
PAFAH2:platelet activating factor acetylhydrolase 2 [Gene - OMIM - HGNC]
PAQR7:progestin and adipoQ receptor family member 7 [Gene - OMIM - HGNC]
SELENON:selenoprotein N [Gene - OMIM - HGNC]
SLC30A2:solute carrier family 30 member 2 [Gene - OMIM - HGNC]
STMN1:stathmin 1 [Gene - OMIM - HGNC]
TRIM63:tripartite motif containing 63 [Gene - OMIM - HGNC]
ZNF593:zinc finger protein 593 [Gene - OMIM - HGNC]
ZNF683:zinc finger protein 683 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1p36.11

Genomic location:

Chr1: 25870180 - 26795632 (on Assembly GRCh37)

Preferred name:

NC_000001.10:g.(?_25870180)_(26795632_?)del

HGVS:

NC_000001.10:g.(?_25870180)_(26795632_?)del

Condition(s)

Name:: Hypercholesterolemia, familial, 4 (FHCL4)
Synonyms:: HYPERCHOLESTEROLEMIA, AUTOSOMAL RECESSIVE, 1; HYPERCHOLESTEROLEMIA, AUTOSOMAL RECESSIVE, 2; Hypercholesterolemia, autosomal recessive
Identifiers:: MONDO: MONDO:0011374; MedGen: C1863512; Orphanet: 391665; OMIM: 603813

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001585077	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 14, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11326085, 12464675, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001585077

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 14, 2020)

germline

clinical testing

PubMed (3)
[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

Autosomal recessive hypercholesterolemia caused by mutations in a putative LDL receptor adaptor protein.

Garcia CK, Wilund K, Arca M, Zuliani G, Fellin R, Maioli M, Calandra S, Bertolini S, Cossu F, Grishin N, Barnes R, Cohen JC, Hobbs HH.

Science. 2001 May 18;292(5520):1394-8. Epub 2001 Apr 26.

PubMed [citation]

PMID:: 11326085

Restoration of LDL receptor function in cells from patients with autosomal recessive hypercholesterolemia by retroviral expression of ARH1.

Eden ER, Patel DD, Sun XM, Burden JJ, Themis M, Edwards M, Lee P, Neuwirth C, Naoumova RP, Soutar AK.

J Clin Invest. 2002 Dec;110(11):1695-702.

PubMed [citation]

PMID:: 12464675
PMCID:: PMC151635

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001585077.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the LDLRAP1 gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals with LDLRAP1-related conditions. Loss-of-function variants in LDLRAP1 are known to be pathogenic (PMID: 11326085, 12464675). 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: Aug 5, 2023

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