SHBG

sex hormone binding globulin

Basic information

Region (hg38): 17:7613945-7633382

Links

ENSG00000129214 ∙ NCBI:6462 ∙ OMIM:182205 ∙ HGNC:10839 ∙ Uniprot:P04278 ∙ 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 SHBG gene.

• Inborn genetic diseases (25 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHBG 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				2	1	3
missense			16	1	3	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8	1	1	10
Total	0	0	24	4	5

Variants in SHBG

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

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

Position	Type	Phenotype	Significance	ClinVar
17-7614519-G-A		not specified	Uncertain significance (Mar 14, 2023)
17-7614523-G-C		not specified	Uncertain significance (Sep 06, 2022)
17-7626488-A-C		not specified	Uncertain significance (Dec 19, 2022)
17-7626549-C-T		not specified	Likely benign (Aug 16, 2022)
17-7626764-T-G		not specified	Uncertain significance (Mar 23, 2022)
17-7626945-C-G		not specified	Uncertain significance (Jan 09, 2024)
17-7627198-A-T		not specified	Uncertain significance (Oct 26, 2021)
17-7627571-C-A		not specified	Uncertain significance (Nov 15, 2023)
17-7627574-A-C		not specified	Uncertain significance (Aug 02, 2022)
17-7627610-G-T		not specified	Uncertain significance (Dec 02, 2021)
17-7627611-C-T		not specified	Uncertain significance (Jan 31, 2023)
17-7627623-G-A		not specified	Uncertain significance (Sep 29, 2023)
17-7627626-C-T		not specified	Uncertain significance (Apr 19, 2023)
17-7630237-G-A			Likely benign (May 30, 2018)
17-7630246-G-A			Benign (Jul 23, 2018)
17-7630419-G-A		not specified	Uncertain significance (Apr 25, 2022)
17-7630424-C-T			Benign (Jul 13, 2018)
17-7630429-C-T		not specified	Uncertain significance (May 11, 2022)
17-7630688-C-G		not specified	Uncertain significance (Jun 28, 2023)
17-7630753-G-T		not specified	Uncertain significance (Dec 21, 2022)
17-7630789-C-A		not specified	Uncertain significance (Dec 06, 2021)
17-7630826-C-T		not specified	Uncertain significance (Jun 29, 2023)
17-7631190-C-G		SHBG-related disorder	Likely benign (Feb 20, 2019)
17-7631215-G-A		not specified	Uncertain significance (Dec 18, 2023)
17-7631245-G-T		not specified	Uncertain significance (Jun 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHBG	protein_coding	protein_coding	ENST00000380450	8	19319

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000125	0.830	125601	0	147	125748	0.000585

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.195	212	220	0.963	0.0000127	2558
Missense in Polyphen		51	55.106	0.92548		716
Synonymous	-0.199	95	92.6	1.03	0.00000513	879
Loss of Function	1.42	12	18.6	0.644	0.00000103	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000275
Ashkenazi Jewish	0.00198	0.00199
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000993	0.000994
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.000651	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as an androgen transport protein, but may also be involved in receptor mediated processes. Each dimer binds one molecule of steroid. Specific for 5-alpha-dihydrotestosterone, testosterone, and 17-beta-estradiol. Regulates the plasma metabolic clearance rate of steroid hormones by controlling their plasma concentration.
• Pathway: Nongenotropic Androgen signaling (Consensus)

Recessive Scores

• pRec: 0.0811

Intolerance Scores

• loftool: 0.226
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

• pHI: 0.0535
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.218

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Shbg

Gene ontology

• Cellular component: extracellular region;extracellular exosome
• Molecular function: steroid binding;androgen binding;protein binding