NM_001360.3(DHCR7):c.1341C>T (p.Asp447=) AND not provided

Germline classification:: Benign/Likely benign (6 submissions)
Last evaluated:: Jul 1, 2024
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:: RCV000512660.41

Allele description [Variation Report for NM_001360.3(DHCR7):c.1341C>T (p.Asp447=)]

NM_001360.3(DHCR7):c.1341C>T (p.Asp447=)

Gene:

DHCR7:7-dehydrocholesterol reductase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.4

Genomic location:

Preferred name:

NM_001360.3(DHCR7):c.1341C>T (p.Asp447=)

HGVS:

NC_000011.10:g.71435462G>A
NG_012655.2:g.17970C>T
NM_001163817.2:c.1341C>T
NM_001360.3:c.1341C>TMANE SELECT
NP_001157289.1:p.Asp447=
NP_001351.2:p.Asp447=
NP_001351.2:p.Asp447=
LRG_340t1:c.1341C>T
LRG_340:g.17970C>T
LRG_340p1:p.Asp447=
NC_000011.9:g.71146508G>A
NM_001163817.1:c.1341C>T
NM_001360.2:c.1341C>T
NP_001351.2:p.(=)
p.Asp447Asp

Links:

dbSNP: rs139721775

NCBI 1000 Genomes Browser:

rs139721775

Molecular consequence:

NM_001163817.2:c.1341C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001360.3:c.1341C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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690495[uid] (1)
Taxonomy
NP_001238793 (0)
Taxonomy
MULTISPECIES: translation elongation factor 4 [Proteus]
MULTISPECIES: translation elongation factor 4 [Proteus]
gi|490364202|ref|WP_004243894.1|

Protein
Profile neighbors for GEO Profiles (Select 38053499) (199)
GEO Profiles
Profile neighbors for GEO Profiles (Select 38047559) (199)
GEO Profiles

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000608603	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Jul 1, 2024)	germline	clinical testing	Citation Link,
SCV000697852	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (May 2, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 12914579, 11241839, 11111101 LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV000883710	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Benign (Jan 9, 2018)	germline	clinical testing	Citation Link,
SCV001870577	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Mar 3, 2015)	germline	clinical testing	Citation Link,
SCV001980498	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV005218383	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	17	not provided	not provided	not provided	not provided	clinical testing, not provided
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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]

PMID:: 12914579

Mutations in the human DHCR7 gene.

Witsch-Baumgartner M, Löffler J, Utermann G.

Hum Mutat. 2001 Mar;17(3):172-82.

PubMed [citation]

PMID:: 11241839

See all PubMed Citations (4)

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV000608603.31

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	17	not provided	not provided	clinical testing	not provided

Description

DHCR7: BP4, BP7, BS2

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		17	not provided	not provided	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000697852.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

Variant summary: The DHCR7 c.1341C>T (p.Asp447Asp) variant involves the alteration of a non-conserved nucleotide causing a synonymous change and 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may eliminate ESE binding sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 399/117638 control chromosomes (6 homozygotes) at a frequency of 0.0033918, which does not exceed the estimated maximal expected allele frequency of a pathogenic DHCR7 variant (0.0043301).Review publications, Jira_2003 and Wareham_2000, classify the variant as a "polymorphism," along with a publication indicating the variant to have been found in a cohort of SLOS patients and classified it as "polymorphism," as well as suggesting the variant may have co-occurred with a deleterious DHCR7 variant. In addition, multiple clinical diagnostic laboratories classified this variant as "likely benign/benign." Taken together, this variant is classified as "likely benign."

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000883710.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV001870577.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is associated with the following publications: (PMID: 28972118)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001980498.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005218383.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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