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NM_001360.3(DHCR7):c.907G>A (p.Gly303Arg)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(2);Pathogenic(5);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Jul 9, 2021)
Last evaluated:
Jun 30, 2021
Accession:
VCV000198773.10
Variation ID:
198773
Description:
single nucleotide variant
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NM_001360.3(DHCR7):c.907G>A (p.Gly303Arg)

Allele ID
195933
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q13.4
Genomic location
11: 71437868 (GRCh38) GRCh38 UCSC
11: 71148914 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.9:g.71148914C>T
LRG_340:g.15564G>A
LRG_340t1:c.907G>A LRG_340p1:p.Gly303Arg
... more HGVS
Protein change
G303R
Other names
-
Canonical SPDI
NC_000011.10:71437867:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00017
Trans-Omics for Precision Medicine (TOPMed) 0.00014
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00031
The Genome Aggregation Database (gnomAD) 0.00013
The Genome Aggregation Database (gnomAD) 0.00014
Links
dbSNP: rs142808899
ClinGen: CA275430
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Oct 13, 2017 RCV000724095.1
Conflicting interpretations of pathogenicity 8 criteria provided, conflicting interpretations Jun 30, 2021 RCV000180217.11
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
DHCR7 - - GRCh38
GRCh37
499 511

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Mar 18, 2016)
criteria provided, single submitter
Method: reference population
Smith-Lemli-Opitz syndrome
Allele origin: germline
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center
Accession: SCV000267288.1
Submitted: (Apr 14, 2016)
Evidence details
Publications
PubMed (1)
Likely pathogenic
(Feb 25, 2016)
criteria provided, single submitter
Method: clinical testing
Smith-Lemli-Opitz syndrome
Allele origin: unknown
Counsyl
Accession: SCV000485874.1
Submitted: (Nov 23, 2016)
Evidence details
Publications
PubMed (2)
Pathogenic
(Oct 13, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000232612.5
Submitted: (Sep 19, 2018)
Evidence details
Publications
PubMed (2)
Other databases
http://www.egl-eurofins.com/emvc…
Likely pathogenic
(Dec 13, 2018)
criteria provided, single submitter
Method: clinical testing
Smith-Lemli-Opitz syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000914537.1
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (3)
Comment:
The DHCR7 c.907G>A (p.Gly303Arg) missense variant has been reported in five studies in which it is found in a compound heterozygous state in six individuals … (more)
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Smith-Lemli-Opitz syndrome
Allele origin: germline
Baylor Genetics
Accession: SCV001163696.1
Submitted: (Sep 27, 2019)
Evidence details
Pathogenic
(Oct 19, 2020)
criteria provided, single submitter
Method: clinical testing
Smith-Lemli-Opitz syndrome
Allele origin: germline
Invitae
Accession: SCV000931749.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change replaces glycine with arginine at codon 303 of the DHCR7 protein (p.Gly303Arg). The glycine residue is highly conserved and there is a … (more)
Pathogenic
(Apr 16, 2021)
criteria provided, single submitter
Method: clinical testing
Smith-Lemli-Opitz syndrome
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001623341.1
Submitted: (May 19, 2021)
Evidence details
Publications
PubMed (5)
Comment:
Variant summary: DHCR7 c.907G>A (p.Gly303Arg) results in a non-conservative amino acid change located in the seventh transmembrane domain, which represent a highly conserved sterol-sensing domain … (more)
Pathogenic
(Jun 30, 2021)
criteria provided, single submitter
Method: clinical testing
Smith-Lemli-Opitz syndrome
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV001752648.1
Submitted: (Jul 09, 2021)
Comment:
This variant has been detected in individual(s) who were sent for testing of Renasight - kidney gene panel.
Evidence details
Pathogenic
(-)
no assertion criteria provided
Method: case-control
Smith-Lemli-Opitz syndrome
Allele origin: inherited
Biochemistry Laboratory of CDMU,Chengde Medical University
Accession: SCV000899187.1
Submitted: (Apr 15, 2019)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Diagnostic Yields of Trio-WES Accompanied by CNVseq for Rare Neurodevelopmental Disorders. Gao C Frontiers in genetics 2019 PMID: 31178897
Novel <i>DHCR7</i> mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development. Tamura M Human genome variation 2017 PMID: 28503313
Prevalence of four Mendelian disorders associated with autism in 2392 affected families. Saskin A Journal of human genetics 2017 PMID: 28250423
A novel DHCR7 mutation in a Smith-Lemli-Opitz syndrome infant presenting with neonatal cholestasis. Ko JS Journal of Korean medical science 2010 PMID: 20052364
R352Q mutation of the DHCR7 gene is common among Japanese Smith-Lemli-Opitz syndrome patients. Matsumoto Y Journal of human genetics 2005 PMID: 16044199
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=DHCR7 - - - -

Text-mined citations for rs142808899...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 04, 2021