NM_001360.3(DHCR7):c.139C>T (p.Leu47=) AND not specified

Clinical significance:Likely benign (Last evaluated: Jun 23, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_001360.3(DHCR7):c.139C>T (p.Leu47=)]

NM_001360.3(DHCR7):c.139C>T (p.Leu47=)

DHCR7:7-dehydrocholesterol reductase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001360.3(DHCR7):c.139C>T (p.Leu47=)
  • NC_000011.10:g.71444175G>A
  • NG_012655.2:g.9257C>T
  • NM_001163817.2:c.139C>T
  • NM_001360.2:c.139C>T
  • NM_001360.3:c.139C>TMANE SELECT
  • NP_001157289.1:p.Leu47=
  • NP_001351.2:p.Leu47=
  • NP_001351.2:p.Leu47=
  • LRG_340t1:c.139C>T
  • LRG_340:g.9257C>T
  • LRG_340p1:p.Leu47=
  • NC_000011.9:g.71155221G>A
dbSNP: rs140721259
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001163817.2:c.139C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001360.2:c.139C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001360.3:c.139C>T - synonymous variant - [Sequence Ontology: SO:0001819]


MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001748825Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Likely benign
(Jun 23, 2021)
germlineclinical testing

PubMed (3)
[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



Smith-Lemli-Opitz syndrome and the DHCR7 gene.

Jira PE, Waterham HR, Wanders RJ, Smeitink JA, Sengers RC, Wevers RA.

Ann Hum Genet. 2003 May;67(Pt 3):269-80. Review.

PubMed [citation]

Mutational spectrum of Smith-Lemli-Opitz syndrome.

Waterham HR, Hennekam RC.

Am J Med Genet C Semin Med Genet. 2012 Nov 15;160C(4):263-84. doi: 10.1002/ajmg.c.31346. Epub 2012 Oct 5. Review.

PubMed [citation]
See all PubMed Citations (3)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001748825.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)


Variant summary: DHCR7 c.139C>T alters a conserved nucleotide resulting in a synonymous change. 4/4 computational tools predict no significant impact on normal splicing while predicting the disruption of ESE binding sites. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 5.9e-05 in 236214 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in DHCR7 causing Smith-Lemli-Opitz Syndrome (5.9e-05 vs 0.0043), allowing no conclusion about variant significance. c.139C>T has been reported in the literature as a polymorphism and/or non pathogenic variant in individuals affected with Smith-Lemli-Opitz Syndrome (example, Witsch-Baumgartner_2001, Jira_2003, Waterham_2012). These report(s) do not provide unequivocal conclusions about association of the variant with Smith-Lemli-Opitz Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (VUS, n=1; likely benign, n=2). Based on the evidence outlined above, the variant was classified as likely benign.

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

Last Updated: Nov 27, 2021

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