NM_000527.5(LDLR):c.1829_1831del (p.Ser610del) AND Familial hypercholesterolemia

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 8, 2019
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:: RCV000791980.9

Allele description [Variation Report for NM_000527.5(LDLR):c.1829_1831del (p.Ser610del)]

NM_000527.5(LDLR):c.1829_1831del (p.Ser610del)

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.1829_1831del (p.Ser610del)

HGVS:

NC_000019.10:g.11116982_11116984del
NG_009060.1:g.32602_32604del
NM_000527.5:c.1829_1831delMANE SELECT
NM_001195798.2:c.1829_1831del
NM_001195799.2:c.1706_1708del
NM_001195800.2:c.1325_1327del
NM_001195803.2:c.1448_1450del
NP_000518.1:p.Ser610del
NP_000518.1:p.Ser610del
NP_001182727.1:p.Ser610del
NP_001182728.1:p.Ser569del
NP_001182729.1:p.Ser442del
NP_001182732.1:p.Ser483del
LRG_274t1:c.1829_1831del
LRG_274:g.32602_32604del
LRG_274p1:p.Ser610del
NC_000019.9:g.11227656_11227658del
NC_000019.9:g.11227658_11227660del
NM_000527.4:c.1829_1831del
NM_000527.5:c.1829_1831delCCTMANE SELECT
c.1829_1831del

Protein change:

S442del

Links:

LDLR-LOVD, British Heart Foundation: LDLR_001528; dbSNP: rs879255037

NCBI 1000 Genomes Browser:

rs879255037

Molecular consequence:

NM_000527.5:c.1829_1831del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001195798.2:c.1829_1831del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001195799.2:c.1706_1708del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001195800.2:c.1325_1327del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001195803.2:c.1448_1450del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Familial hypercholesterolemia
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
SCV000931251	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Jan 8, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 20809525, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000931251

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Jan 8, 2019)

germline

clinical testing

PubMed (2)
[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

Molecular spectrum of autosomal dominant hypercholesterolemia in France.

Marduel M, Carrié A, Sassolas A, Devillers M, Carreau V, Di Filippo M, Erlich D, Abifadel M, Marques-Pinheiro A, Munnich A, Junien C; French ADH Research Network., Boileau C, Varret M, Rabès JP.

Hum Mutat. 2010 Nov;31(11):E1811-24. doi: 10.1002/humu.21348.

PubMed [citation]

PMID:: 20809525
PMCID:: PMC3152176

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000931251.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant has been observed in several individuals affected with hypercholesterolemia (PMID: 20809525,¬†29572815, Invitae). ClinVar contains an entry for this variant (Variation ID: 252053). This variant is not present in population databases (ExAC no frequency). This variant, c.1829_1831del, results in the deletion of 1 amino acid(s) of the LDLR protein (p.Ser610del), but otherwise preserves the integrity of the reading frame.

#	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: Sep 29, 2024

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