CGB5

chorionic gonadotropin subunit beta 5, the group of Glycoprotein hormone subunits

Basic information

Region (hg38): 19:49043848-49045311

Links

ENSG00000189052 ∙ NCBI:93659 ∙ OMIM:608825 ∙ HGNC:16452 ∙ Uniprot:P0DN86 ∙ 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 CGB5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CGB5 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	1	2
missense			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	1

Variants in CGB5

This is a list of pathogenic ClinVar variants found in the CGB5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49044610-G-C		not specified	Uncertain significance (Sep 20, 2024)
19-49044626-A-G		not specified	Likely benign (Feb 22, 2023)
19-49044633-G-A			Benign (Dec 31, 2019)
19-49044638-G-A		not specified	Uncertain significance (Mar 01, 2024)
19-49044644-G-A		not specified	Uncertain significance (Nov 26, 2024)
19-49044650-G-A		not specified	Uncertain significance (Jan 12, 2024)
19-49044665-C-T		not specified	Uncertain significance (Mar 11, 2025)
19-49044706-G-A		not specified	Uncertain significance (Sep 20, 2023)
19-49044731-A-T		not specified	Uncertain significance (Apr 23, 2024)
19-49044743-T-G		not specified	Uncertain significance (Apr 06, 2023)
19-49045023-T-C		not specified	Uncertain significance (Oct 13, 2021)
19-49045029-A-C		not specified	Likely benign (Mar 30, 2024)
19-49045043-C-A		not specified	Uncertain significance (Nov 24, 2024)
19-49045068-G-T		not specified	Uncertain significance (Jan 26, 2022)
19-49045102-C-T			Likely benign (Jun 12, 2018)
19-49045136-C-T		not specified	Uncertain significance (Aug 20, 2024)
19-49045175-C-G		not specified	Uncertain significance (Jun 03, 2024)
19-49045192-C-G		not specified	Uncertain significance (Jan 03, 2025)
19-49045211-T-C		not specified	Uncertain significance (Apr 27, 2024)
19-49045224-C-G		not specified	Uncertain significance (Mar 07, 2025)
19-49045232-C-G		not specified	Uncertain significance (Jan 29, 2024)
19-49045233-C-G		not specified	Uncertain significance (Feb 11, 2025)
19-49045237-C-G		not specified	Uncertain significance (Mar 07, 2023)
19-49045263-G-A		not specified	Likely benign (Jan 27, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CGB5	protein_coding	protein_coding	ENST00000301408	3	1428

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0254	0.576	125321	0	7	125328	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.584	72	59.3	1.21	0.00000430	1039
Missense in Polyphen		23	26.294	0.87471		497
Synonymous	-1.08	31	24.2	1.28	0.00000165	368
Loss of Function	0.0128	2	2.02	0.990	8.62e-8	36

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000884	0.00000884
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Beta subunit of the human chorionic gonadotropin (hCG). hCG is a complex glycoprotein composed of two glycosylated subunits alpha and beta which are non-covalently associated. The alpha subunit is identical to those in the pituitary gonadotropin hormones (LH, FSH and TSH). The beta subunits are distinct in each of the hormones and confer receptor and biological specificity. Has an essential role in pregnancy and maternal adaptation. Stimulates the ovaries to synthesize the steroids that are essential for the maintenance of pregnancy. {ECO:0000305}.
• Pathway: Gene expression (Transcription);Peptide hormone metabolism;Generic Transcription Pathway;Metabolism of proteins;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;RNA Polymerase II Transcription;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;TFAP2 (AP-2) family regulates transcription of growth factors and their receptors;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors;GPCR signaling-G alpha i;Glycoprotein hormones;Peptide hormone biosynthesis (Consensus)

Recessive Scores

• pRec: 0.150

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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