NM_000527.5(LDLR):c.2289G>T (p.Glu763Asp) AND Familial hypercholesterolemia

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Jan 21, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000776247.13

Allele description [Variation Report for NM_000527.5(LDLR):c.2289G>T (p.Glu763Asp)]

NM_000527.5(LDLR):c.2289G>T (p.Glu763Asp)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NM_000527.5(LDLR):c.2289G>T (p.Glu763Asp)

HGVS:

NC_000019.10:g.11123322G>T
NG_009060.1:g.38942G>T
NM_000527.5:c.2289G>TMANE SELECT
NM_001195798.2:c.2289G>T
NM_001195799.2:c.2166G>T
NM_001195800.2:c.1785G>T
NM_001195803.2:c.1755G>T
NP_000518.1:p.Glu763Asp
NP_000518.1:p.Glu763Asp
NP_001182727.1:p.Glu763Asp
NP_001182728.1:p.Glu722Asp
NP_001182729.1:p.Glu595Asp
NP_001182732.1:p.Glu585Asp
LRG_274t1:c.2289G>T
LRG_274:g.38942G>T
LRG_274p1:p.Glu763Asp
NC_000019.9:g.11233998G>T
NM_000527.4:c.2289G>T
c.2289G>T

Protein change:

E585D

Links:

LDLR-LOVD, British Heart Foundation: LDLR_001621; dbSNP: rs774698247

NCBI 1000 Genomes Browser:

rs774698247

Molecular consequence:

NM_000527.5:c.2289G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001195798.2:c.2289G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001195799.2:c.2166G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001195800.2:c.1785G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001195803.2:c.1755G>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000911499	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jan 23, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001012665	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 21, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002086872	Natera, Inc.	no assertion criteria provided	Likely benign (Jan 31, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000911499

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Jan 23, 2020)

germline

clinical testing

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

SCV001012665

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 21, 2024)

germline

clinical testing

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

SCV002086872

Natera, Inc.

no assertion criteria provided

Likely benign
(Jan 31, 2020)

germline

clinical testing

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

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 Color Diagnostics, LLC DBA Color Health, SCV000911499.2

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

#	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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001012665.6

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

#	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

From Natera, Inc., SCV002086872.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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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