NM_000527.5(LDLR):c.1959T>C (p.Val653=) AND Hypercholesterolemia, familial, 1

Germline classification:: Benign/Likely benign (7 submissions)
Last evaluated:: Jun 10, 2021
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:: RCV000238160.23

Allele description [Variation Report for NM_000527.5(LDLR):c.1959T>C (p.Val653=)]

NM_000527.5(LDLR):c.1959T>C (p.Val653=)

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.1959T>C (p.Val653=)

HGVS:

NC_000019.10:g.11120205T>C
NG_009060.1:g.35825T>C
NM_000527.5:c.1959T>CMANE SELECT
NM_001195798.2:c.1959T>C
NM_001195799.2:c.1836T>C
NM_001195800.2:c.1455T>C
NM_001195803.2:c.1578T>C
NP_000518.1:p.Val653=
NP_000518.1:p.Val653=
NP_001182727.1:p.Val653=
NP_001182728.1:p.Val612=
NP_001182729.1:p.Val485=
NP_001182732.1:p.Val526=
LRG_274t1:c.1959T>C
LRG_274:g.35825T>C
LRG_274p1:p.Val653=
NC_000019.9:g.11230881T>C
NM_000527.4:c.1959T>C
c.1959T>C
p.Val653Val

Links:

LDLR-LOVD, British Heart Foundation: LDLR_001191; dbSNP: rs5925

NCBI 1000 Genomes Browser:

rs5925

Molecular consequence:

NM_000527.5:c.1959T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001195798.2:c.1959T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001195799.2:c.1836T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001195800.2:c.1455T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001195803.2:c.1578T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Name:: Hypercholesterolemia, familial, 1
Synonyms:: LDL RECEPTOR DISORDER; Hyperlipoproteinemia Type IIa; HYPER-LOW-DENSITY-LIPOPROTEINEMIA; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007750; MedGen: C0745103; Orphanet: 391665; OMIM: 143890

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CR418082 XGC-tailbud Xenopus tropicalis cDNA clone TTbA018h17 5', mRNA sequence
CR418082 XGC-tailbud Xenopus tropicalis cDNA clone TTbA018h17 5', mRNA sequence
gi|48686329|gnl|dbEST|23655802|emb| 082.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000295777	LDLR-LOVD, British Heart Foundation	criteria provided, single submitter (ACGS Guidelines, 2013)	Benign (Mar 25, 2016)	germline	literature only	PubMed (3) [See all records that cite these PMIDs] 12730724, 24373485, 26892515 Citation Link,
SCV000322991	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Mar 1, 2016)	germline	research	PubMed (1) [See all records that cite this PMID]
SCV000410539	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Mar 6, 2018)	germline	clinical testing	Citation Link,
SCV000606563	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	no assertion criteria provided	Benign	germline	research
SCV000689770	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jun 22, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000987009	Department of Human Genetics, Laborarztpraxis Dres. Walther, Weindel und Kollegen	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jul 16, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001738024	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jun 10, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, research
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing, research
not provided	germline	no	3	not provided	not provided	3	not provided	clinical testing, literature only

Citations

PubMed

Familial hypercholesterolemia in Morocco: first report of mutations in the LDL receptor gene.

El Messal M, Aït Chihab K, Chater R, Vallvé JC, Bennis F, Hafidi A, Ribalta J, Varret M, Loutfi M, Rabès JP, Kettani A, Boileau C, Masana L, Adlouni A.

J Hum Genet. 2003;48(4):199-203. Epub 2003 Mar 18.

PubMed [citation]

PMID:: 12730724

Familial hypercholesterolemia mutations in Petrozavodsk: no similarity to St. Petersburg mutation spectrum.

Komarova TY, Korneva VA, Kuznetsova TY, Golovina AS, Vasilyev VB, Mandelshtam MY.

BMC Med Genet. 2013 Dec 27;14:128. doi: 10.1186/1471-2350-14-128.

PubMed [citation]

PMID:: 24373485
PMCID:: PMC3877960

See all PubMed Citations (4)

Details of each submission

From LDLR-LOVD, British Heart Foundation, SCV000295777.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	literature only	PubMed (3)
2	not provided	1	not provided	not provided	literature only	PubMed (3)
3	not provided	1	not provided	not provided	literature only	PubMed (3)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	1	not provided	not provided		1	not provided	not provided	not provided
2	germline	no	1	not provided	not provided		1	not provided	not provided	not provided
3	germline	no	1	not provided	not provided		1	not provided	not provided	not provided

From Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge, SCV000322991.1

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

Description

%MAF (ExAC):40.92

Description

MAF = 48,3% in 86 Spanish healthy individuals

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

From Illumina Laboratory Services, Illumina, SCV000410539.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	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 Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum, SCV000606563.1

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

From Color Diagnostics, LLC DBA Color Health, SCV000689770.2

#	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 Department of Human Genetics, Laborarztpraxis Dres. Walther, Weindel und Kollegen, SCV000987009.1

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

Description

Due to the increased occurrence of the mutation (>= 5%) and the current estimates of databases (LOVD 3), this variant is classified as likely benign.

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

From Genome-Nilou Lab, SCV001738024.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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