CGB3

chorionic gonadotropin subunit beta 3, the group of Receptor ligands|Glycoprotein hormone subunits

Basic information

Region (hg38): 19:49022869-49024333

Previous symbols: [ "CGB" ]

Links

ENSG00000104827 ∙ NCBI:1082 ∙ OMIM:118860 ∙ HGNC:1886 ∙ 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 CGB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CGB3 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		2
missense			2	1		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	3	0

Variants in CGB3

This is a list of pathogenic ClinVar variants found in the CGB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49022974-T-C		not specified	Uncertain significance (Sep 17, 2021)
19-49023006-G-A			Likely benign (Jan 01, 2023)
19-49023024-G-A			Likely benign (Dec 01, 2023)
19-49023530-C-T		not specified	Uncertain significance (Aug 12, 2021)
19-49023962-A-G		not specified	Likely benign (Oct 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CGB3	protein_coding	protein_coding	ENST00000357383	3	1465

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0983	0.596	125487	0	18	125505	0.0000717

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.942	61	43.5	1.40	0.00000296	1014
Missense in Polyphen		20	17.202	1.1627		482
Synonymous	-1.85	27	17.2	1.57	0.00000107	356
Loss of Function	0.123	1	1.14	0.876	4.90e-8	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

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: Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors;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: 0.0967

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.459

Essentials

• essential_gene_gene_trap: N

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;apoptotic process;signal transduction;G protein-coupled receptor signaling pathway;cell-cell signaling;female gamete generation;hormone-mediated signaling pathway;regulation of signaling receptor activity;peptide hormone processing
• Cellular component: extracellular region;extracellular space;cytoplasm
• Molecular function: hormone activity