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

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Oct 11, 2022
Review status:
criteria provided, conflicting classifications
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:
RCV000775024.17

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)

Name:
Familial hypercholesterolemia
Identifiers:
MONDO: MONDO:0005439; MedGen: C0020445; OMIM: PS143890

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000285020Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jul 26, 2022)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

SCV000909121Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(Oct 11, 2022)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

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

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
See all PubMed Citations (8)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000285020.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 62 of the LDLR protein (p.Thr62Met). This variant is present in population databases (rs376207800, gnomAD 0.02%). This missense change has been observed in individual(s) with hypercholesterolemia (PMID: 16250003, 19446849, 19717150, 25606447, 26892515, 33303402). This variant is also known as p.Thr41Met. ClinVar contains an entry for this variant (Variation ID: 161273). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

From Color Diagnostics, LLC DBA Color Health, SCV000909121.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024