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NM_000527.5(LDLR):c.1323C>T (p.Ile441=) AND not specified

Germline classification:
Benign (2 submissions)
Last evaluated:
Nov 22, 2019
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:
RCV000781494.4

Allele description [Variation Report for NM_000527.5(LDLR):c.1323C>T (p.Ile441=)]

NM_000527.5(LDLR):c.1323C>T (p.Ile441=)

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.1323C>T (p.Ile441=)
Other names:
NM_000527.4(LDLR):c.1323C>T; p.Ile441=
HGVS:
  • NC_000019.10:g.11113414C>T
  • NG_009060.1:g.29034C>T
  • NM_000527.5:c.1323C>TMANE SELECT
  • NM_001195798.2:c.1323C>T
  • NM_001195799.2:c.1200C>T
  • NM_001195800.2:c.819C>T
  • NM_001195803.2:c.942C>T
  • NP_000518.1:p.Ile441=
  • NP_000518.1:p.Ile441=
  • NP_001182727.1:p.Ile441=
  • NP_001182728.1:p.Ile400=
  • NP_001182729.1:p.Ile273=
  • NP_001182732.1:p.Ile314=
  • LRG_274t1:c.1323C>T
  • LRG_274:g.29034C>T
  • LRG_274p1:p.Ile441=
  • NC_000019.9:g.11224090C>T
  • NM_000527.4:c.1323C>T
Links:
dbSNP: rs5933
NCBI 1000 Genomes Browser:
rs5933
Molecular consequence:
  • NM_000527.5:c.1323C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195798.2:c.1323C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195799.2:c.1200C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195800.2:c.819C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195803.2:c.942C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000919572Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(Oct 12, 2017) 		germlineclinical testing

Citation Link,

SCV001470527Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)		Benign
(Nov 22, 2019) 		unknownclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000919572.1

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

Description

Variant summary: The LDLR c.1323C>T (p.Ile441Ile) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 121/277028 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.004829 (116/24020). This frequency is about 4 times the estimated maximal expected allele frequency of a pathogenic LDLR variant (0.0012508), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. An internal LCA sample also carried a pathogenic variant LDLR c.590G>A/ p.Cys197Tyr, further supporting the benign nature of this variant. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories. Taken together, this variant is classified as benign.

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001470527.1

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

Last Updated: Oct 8, 2024