SRD5A1

steroid 5 alpha-reductase 1, the group of Steroid 5-alpha reductase family

Basic information

Region (hg38): 5:6633290-6676539

Links

ENSG00000145545 ∙ NCBI:6715 ∙ OMIM:184753 ∙ HGNC:11284 ∙ Uniprot:P18405 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SRD5A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRD5A1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	3	4
missense			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	3	3

Variants in SRD5A1

This is a list of pathogenic ClinVar variants found in the SRD5A1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-6633319-G-A		Intellectual Disability, Recessive	Conflicting classifications of pathogenicity (Sep 11, 2018)
5-6633321-G-A		Intellectual Disability, Recessive	Uncertain significance (Jun 14, 2016)
5-6633334-C-T		Intellectual Disability, Recessive	Benign (Oct 01, 2018)
5-6633392-G-A			Likely benign (Jan 28, 2019)
5-6633401-C-T			Likely benign (May 03, 2019)
5-6633581-C-T		not specified	Uncertain significance (Nov 09, 2021)
5-6633595-G-A		not specified	Uncertain significance (Mar 07, 2024)
5-6633640-G-A		not specified	Uncertain significance (Jul 25, 2023)
5-6633649-T-C		not specified	Uncertain significance (Jan 30, 2024)
5-6633651-C-G		not specified	Uncertain significance (Dec 20, 2023)
5-6633666-C-G			Benign (Sep 11, 2018)
5-6633676-A-G		not specified	Uncertain significance (Dec 16, 2021)
5-6633686-T-C		not specified	Likely benign (Apr 28, 2022)
5-6633731-C-T		not specified	Uncertain significance (Apr 06, 2022)
5-6633736-G-A		not specified	Uncertain significance (Sep 25, 2023)
5-6633748-G-C		not specified	Likely benign (Jan 29, 2024)
5-6633782-A-G		not specified	Uncertain significance (Apr 08, 2024)
5-6633811-C-G		not specified	Uncertain significance (Dec 03, 2021)
5-6651908-G-A			Likely benign (Jul 05, 2018)
5-6651940-A-G		not specified	Uncertain significance (May 09, 2022)
5-6651970-A-C		not specified	Uncertain significance (Nov 07, 2023)
5-6652005-A-G		not specified	Uncertain significance (Jan 18, 2023)
5-6656094-A-G			Benign (May 03, 2018)
5-6656126-A-T		not specified	Uncertain significance (Oct 13, 2023)
5-6656129-T-C		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRD5A1	protein_coding	protein_coding	ENST00000274192	5	36220

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000116	0.606	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.590	129	149	0.864	0.00000748	1653
Missense in Polyphen		39	51.169	0.76217		620
Synonymous	-1.09	71	60.2	1.18	0.00000312	505
Loss of Function	0.844	9	12.2	0.739	6.08e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000602	0.0000602
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000947	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Converts testosterone into 5-alpha-dihydrotestosterone and progesterone or corticosterone into their corresponding 5- alpha-3-oxosteroids. It plays a central role in sexual differentiation and androgen physiology.
• Pathway: Steroid hormone biosynthesis - Homo sapiens (human);17-Beta Hydroxysteroid Dehydrogenase III Deficiency;Androgen and Estrogen Metabolism;Aromatase deficiency;Metabolism of lipids;Androgen and estrogen biosynthesis and metabolism;Metabolism;allopregnanolone biosynthesis;Androgen biosynthesis;Metabolism of steroid hormones;Metabolism of steroids;Bile acid biosynthesis;androgen biosynthesis;superpathway of steroid hormone biosynthesis;Steroid hormones (Consensus)

Intolerance Scores

• loftool: 0.612
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.0587
• hipred: N
• hipred_score: 0.271
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.954

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Srd5a1
• Phenotype: endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: urogenital system development;liver development;steroid biosynthetic process;androgen biosynthetic process;androgen catabolic process;sex determination;male gonad development;cellular response to starvation;response to muscle activity;diterpenoid metabolic process;spinal cord development;hippocampus development;thalamus development;hypothalamus development;pituitary gland development;cerebral cortex development;electron transport chain;cell differentiation;male genitalia development;female genitalia development;response to follicle-stimulating hormone;cellular response to insulin stimulus;serotonin metabolic process;progesterone metabolic process;circadian sleep/wake cycle, REM sleep;response to estrogen;bone development;response to growth hormone;response to fungicide;cellular response to cAMP;cellular response to growth factor stimulus;cellular response to estradiol stimulus;cellular response to testosterone stimulus;cellular response to dexamethasone stimulus;cellular response to epinephrine stimulus
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;organelle membrane;neuronal cell body;myelin sheath;perinuclear region of cytoplasm;cell body fiber
• Molecular function: 3-oxo-5-alpha-steroid 4-dehydrogenase activity;electron transfer activity;oxidoreductase activity;amide binding;cholestenone 5-alpha-reductase activity;NADPH binding