NM_000198.4(HSD3B2):c.15C>A (p.Cys5Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 18, 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:: RCV001390355.5

Allele description [Variation Report for NM_000198.4(HSD3B2):c.15C>A (p.Cys5Ter)]

NM_000198.4(HSD3B2):c.15C>A (p.Cys5Ter)

Genes:

LOC109029530:HSD3B2 5' regulatory region [Gene]
HSD3B2:hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p12

Genomic location:

Preferred name:

NM_000198.4(HSD3B2):c.15C>A (p.Cys5Ter)

HGVS:

NC_000001.11:g.119415434C>A
NG_013349.1:g.5504C>A
NG_052011.1:g.1458C>A
NM_000198.4:c.15C>AMANE SELECT
NM_001166120.2:c.15C>A
NP_000189.1:p.Cys5Ter
NP_001159592.1:p.Cys5Ter
NC_000001.10:g.119958057C>A

Protein change:

C5*

Links:

dbSNP: rs766474996

NCBI 1000 Genomes Browser:

rs766474996

Molecular consequence:

NM_000198.4:c.15C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001166120.2:c.15C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001592041	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 18, 2024)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11196452, 31611844, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001592041

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 18, 2024)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

A new insight into the molecular basis of 3beta-hydroxysteroid dehydrogenase deficiency.

Simard J, Ricketts ML, Moisan AM, Tardy V, Peter M, Van Vliet G, Morel Y.

Endocr Res. 2000 Nov;26(4):761-70. Review.

PubMed [citation]

PMID:: 11196452

Coexistence of Congenital Adrenal Hyperplasia and Autoimmune Addison's Disease.

Aslaksen S, Methlie P, Vigeland MD, Jøssang DE, Wolff AB, Sheng Y, Oftedal BE, Skinningsrud B, Undlien DE, Selmer KK, Husebye ES, Bratland E.

Front Endocrinol (Lausanne). 2019;10:648. doi: 10.3389/fendo.2019.00648.

PubMed [citation]

PMID:: 31611844
PMCID:: PMC6776599

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001592041.4

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

Description

This sequence change creates a premature translational stop signal (p.Cys5*) in the HSD3B2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in HSD3B2 are known to be pathogenic (PMID: 11196452). This variant is present in population databases (rs766474996, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with 3-beta-hydroxysteroid dehydrogenase deficiency (PMID: 31611844). ClinVar contains an entry for this variant (Variation ID: 1076441). For these reasons, this variant has been classified as Pathogenic.

#	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

Last Updated: Sep 29, 2024

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