NM_000527.5(LDLR):c.313+3A>C AND not provided

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jan 13, 2023
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:: RCV000482458.10

Allele description [Variation Report for NM_000527.5(LDLR):c.313+3A>C]

NM_000527.5(LDLR):c.313+3A>C

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.313+3A>C

HGVS:

NC_000019.10:g.11102789A>C
NG_009060.1:g.18409A>C
NM_000527.5:c.313+3A>CMANE SELECT
NM_001195798.2:c.313+3A>C
NM_001195799.2:c.191-2431A>C
NM_001195800.2:c.313+3A>C
NM_001195803.2:c.313+3A>C
LRG_274t1:c.313+3A>C
LRG_274:g.18409A>C
NC_000019.9:g.11213465A>C
NM_000527.4:c.313+3A>C

Links:

dbSNP: rs1064793799

NCBI 1000 Genomes Browser:

rs1064793799

Molecular consequence:

NM_000527.5:c.313+3A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001195798.2:c.313+3A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001195799.2:c.191-2431A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001195800.2:c.313+3A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001195803.2:c.313+3A>C - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000567065	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Jan 13, 2023)	germline	clinical testing	Citation Link,
SCV001715236	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Aug 31, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 30919572, 35910211, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000567065

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Jan 13, 2023)

germline

clinical testing

Citation Link,

SCV001715236

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Aug 31, 2022)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical exome sequencing in 509 Middle Eastern families with suspected Mendelian diseases: The Qatari experience.

Al-Dewik N, Mohd H, Al-Mureikhi M, Ali R, Al-Mesaifri F, Mahmoud L, Shahbeck N, El-Akouri K, Almulla M, Al Sulaiman R, Musa S, Al-Marri AA, Richard G, Juusola J, Solomon BD, Alkuraya FS, Ben-Omran T.

Am J Med Genet A. 2019 Jun;179(6):927-935. doi: 10.1002/ajmg.a.61126. Epub 2019 Mar 27.

PubMed [citation]

PMID:: 30919572
PMCID:: PMC6916397

The Prevalence and Genetic Spectrum of Familial Hypercholesterolemia in Qatar Based on Whole Genome Sequencing of 14,000 Subjects.

Diboun I, Al-Sarraj Y, Toor SM, Mohammed S, Qureshi N, Al Hail MSH, Jayyousi A, Al Suwaidi J, Albagha OME.

Front Genet. 2022;13:927504. doi: 10.3389/fgene.2022.927504.

PubMed [citation]

PMID:: 35910211
PMCID:: PMC9337875

See all PubMed Citations (3)

Details of each submission

From GeneDx, SCV000567065.6

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

Description

Not observed in large population cohorts (gnomAD); Splice variants and deletions involving coding exons in this gene are frequently reported as pathogenic, regardless of frame prediction (HGMD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 30919572, 34428338)

#	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 Mayo Clinic Laboratories, Mayo Clinic, SCV001715236.2

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

Description

PP3, PM1, PM2_supporting, PS4

#	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		2	not provided	not provided	not provided

Last Updated: Jun 23, 2024

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