NM_001360.3(DHCR7):c.1141T>C (p.Ser381Pro) AND Smith-Lemli-Opitz syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 29, 2024
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:: RCV004527561.1

Allele description [Variation Report for NM_001360.3(DHCR7):c.1141T>C (p.Ser381Pro)]

NM_001360.3(DHCR7):c.1141T>C (p.Ser381Pro)

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.1141T>C (p.Ser381Pro)

Other names:

p.Ser381Pro

HGVS:

NC_000011.10:g.71435662A>G
NG_012655.2:g.17770T>C
NM_001163817.2:c.1141T>C
NM_001360.3:c.1141T>CMANE SELECT
NM_001425107.1:c.1192T>C
NM_001425108.1:c.1177T>C
NM_001425109.1:c.1141T>C
NM_001425110.1:c.1141T>C
NM_001425111.1:c.1141T>C
NM_001425112.1:c.1275T>C
NM_001425113.1:c.1081T>C
NM_001425114.1:c.1045T>C
NM_001425116.1:c.1179T>C
NM_001425117.1:c.967T>C
NM_001425119.1:c.*263T>C
NP_001157289.1:p.Ser381Pro
NP_001351.2:p.Ser381Pro
NP_001351.2:p.Ser381Pro
NP_001412036.1:p.Ser398Pro
NP_001412037.1:p.Ser393Pro
NP_001412038.1:p.Ser381Pro
NP_001412039.1:p.Ser381Pro
NP_001412040.1:p.Ser381Pro
NP_001412041.1:p.Ala425=
NP_001412042.1:p.Ser361Pro
NP_001412043.1:p.Ser349Pro
NP_001412045.1:p.Ala393=
NP_001412046.1:p.Ser323Pro
LRG_340t1:c.1141T>C
LRG_340:g.17770T>C
LRG_340p1:p.Ser381Pro
NC_000011.9:g.71146708A>G
NM_001360.2:c.1141T>C

Protein change:

S323P

Molecular consequence:

NM_001163817.2:c.1141T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001360.3:c.1141T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425107.1:c.1192T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425108.1:c.1177T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425109.1:c.1141T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425110.1:c.1141T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425111.1:c.1141T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425113.1:c.1081T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425114.1:c.1045T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425117.1:c.967T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425112.1:c.1275T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001425116.1:c.1179T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Name:: Smith-Lemli-Opitz syndrome (SLOS)
Synonyms:: LETHAL ACRODYSGENITAL SYNDROME; POLYDACTYLY, SEX REVERSAL, RENAL HYPOPLASIA, AND UNILOBAR LUNG; RUTLEDGE LETHAL MULTIPLE CONGENITAL ANOMALY SYNDROME; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010035; MedGen: C0175694; Orphanet: 818; OMIM: 270400

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005038958	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 29, 2024)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005038958

Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Apr 29, 2024)

de novo

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV005038958.1

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

Description

A homozygous missense variant in exon 9 of the DHCR7 gene that results in the amino acid substitution of Proline for Serine at codon 381 (p.Ser381Pro) was detected. The observed variant has not been reported in the 1000 genomes, gnomAD (v3.1), gnomdAD (v2.1) and topmed databases. The in silico prediction of the variant are probably damaging by PolyPhen-2 (HumDiv) and damaging by SIFT. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as variant of uncertain significance.

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

Last Updated: Sep 1, 2024

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