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NM_000527.5(LDLR):c.185C>T (p.Thr62Met) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 2, 2024
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:
RCV000454406.14

Allele description [Variation Report for NM_000527.5(LDLR):c.185C>T (p.Thr62Met)]

NM_000527.5(LDLR):c.185C>T (p.Thr62Met)

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.185C>T (p.Thr62Met)
Other names:
NM_000527.5(LDLR):c.185C>T
HGVS:
  • NC_000019.10:g.11100340C>T
  • NG_009060.1:g.15960C>T
  • NM_000527.5:c.185C>TMANE SELECT
  • NM_001195798.2:c.185C>T
  • NM_001195799.2:c.185C>T
  • NM_001195800.2:c.185C>T
  • NM_001195803.2:c.185C>T
  • NP_000518.1:p.Thr62Met
  • NP_000518.1:p.Thr62Met
  • NP_001182727.1:p.Thr62Met
  • NP_001182728.1:p.Thr62Met
  • NP_001182729.1:p.Thr62Met
  • NP_001182732.1:p.Thr62Met
  • LRG_274t1:c.185C>T
  • LRG_274:g.15960C>T
  • LRG_274p1:p.Thr62Met
  • NC_000019.9:g.11211016C>T
  • NM_000527.4:c.185C>T
  • c.185C>T
Protein change:
T62M
Links:
LDLR-LOVD, British Heart Foundation: LDLR_001030;
Molecular consequence:
  • NM_000527.5:c.185C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195798.2:c.185C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195799.2:c.185C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195800.2:c.185C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195803.2:c.185C>T - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
no known functional consequence - Comment(s)

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004241787Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Uncertain significance
(Jul 2, 2024)
germlineclinical testing

PubMed (10)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

The type of LDLR gene mutation predicts cardiovascular risk in children with familial hypercholesterolemia.

Guardamagna O, Restagno G, Rolfo E, Pederiva C, Martini S, Abello F, Baracco V, Pisciotta L, Pino E, Calandra S, Bertolini S.

J Pediatr. 2009 Aug;155(2):199-204.e2. doi: 10.1016/j.jpeds.2009.02.022. Epub 2009 May 15.

PubMed [citation]
PMID:
19446849

Update of the molecular basis of familial hypercholesterolemia in The Netherlands.

Fouchier SW, Kastelein JJ, Defesche JC.

Hum Mutat. 2005 Dec;26(6):550-6.

PubMed [citation]
PMID:
16250003
See all PubMed Citations (10)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004241787.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (10)

Description

Variant summary: LDLR c.185C>T (p.Thr62Met) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00012 in 250804 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in LDLR causing Familial Hypercholesterolemia (0.00012 vs 0.0013), allowing no conclusion about variant significance. c.185C>T has been reported in the literature in individuals affected with Familial Hypercholesterolemia (Fouchier_2005, Guardamagna_2009, Junyent_2010, Cymbron_2014, Sharifi_2016, Gill_2020). These reports do not provide unequivocal conclusions about association of the variant with Familial Hypercholesterolemia. Functional studies report experimental evidence evaluating an impact on protein function. These results showed no damaging effect of this variant (Thormaehlen_2015, Benito-Vicente_2018, Graca_2020). The following publications have been ascertained in the context of this evaluation (PMID: 30413722, 25606447, 16250003, 33303402, 35568682, 19446849, 19717150, 34456049, 26892515, 25647241). ClinVar contains an entry for this variant (Variation ID: 161273). Based on the evidence outlined above, the variant was classified as uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024