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NM_000527.5(LDLR):c.139G>T (p.Asp47Tyr) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 21, 2021
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:
RCV001290542.2

Allele description [Variation Report for NM_000527.5(LDLR):c.139G>T (p.Asp47Tyr)]

NM_000527.5(LDLR):c.139G>T (p.Asp47Tyr)

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.139G>T (p.Asp47Tyr)
Other names:
NM_000527.5(LDLR):c.139G>T; p.Asp47Tyr
HGVS:
  • NC_000019.10:g.11100294G>T
  • NG_009060.1:g.15914G>T
  • NM_000527.5:c.139G>TMANE SELECT
  • NM_001195798.2:c.139G>T
  • NM_001195799.2:c.139G>T
  • NM_001195800.2:c.139G>T
  • NM_001195803.2:c.139G>T
  • NP_000518.1:p.Asp47Tyr
  • NP_001182727.1:p.Asp47Tyr
  • NP_001182728.1:p.Asp47Tyr
  • NP_001182729.1:p.Asp47Tyr
  • NP_001182732.1:p.Asp47Tyr
  • LRG_274t1:c.139G>T
  • LRG_274:g.15914G>T
  • NC_000019.9:g.11210970G>T
  • NM_000527.4:c.139G>T
Protein change:
D47Y
Links:
dbSNP: rs778284147
NCBI 1000 Genomes Browser:
rs778284147
Molecular consequence:
  • NM_000527.5:c.139G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195798.2:c.139G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195799.2:c.139G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195800.2:c.139G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195803.2:c.139G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001478603Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Jan 21, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001478603.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: LDLR c.139G>T (p.Asp47Tyr) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251226 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.139G>T in individuals affected with Familial Hypercholesterolemia and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. 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: Aug 5, 2023