CGB2

chorionic gonadotropin subunit beta 2, the group of Glycoprotein hormone subunits

Basic information

Region (hg38): 19:49031890-49033238

Links

ENSG00000104818 ∙ NCBI:114336 ∙ OMIM:608824 ∙ HGNC:16722 ∙ Uniprot:Q6NT52 ∙ 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 CGB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CGB2 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
missense			10	3	1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	4	1

Variants in CGB2

This is a list of pathogenic ClinVar variants found in the CGB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49032537-G-A		not specified	Uncertain significance (Dec 13, 2021)
19-49032549-T-C		not specified	Uncertain significance (Aug 10, 2021)
19-49032570-C-T		not specified	Uncertain significance (Dec 07, 2021)
19-49032592-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-49032636-A-G		not specified	Uncertain significance (Mar 06, 2023)
19-49032937-C-G		not specified	Likely benign (Sep 06, 2022)
19-49033048-C-A		not specified	Uncertain significance (May 01, 2024)
19-49033049-A-G		not specified	Likely benign (Feb 07, 2023)
19-49033050-A-C		not specified	Likely benign (Feb 07, 2023)
19-49033057-C-T		not specified	Uncertain significance (Sep 12, 2023)
19-49033119-C-A		not specified	Uncertain significance (Mar 13, 2023)
19-49033133-C-A			Benign (Feb 02, 2018)
19-49033151-C-G		not specified	Uncertain significance (Jan 05, 2022)
19-49033156-C-T		not specified	Uncertain significance (Sep 29, 2023)
19-49033192-C-T		not specified	Uncertain significance (May 05, 2023)
19-49033197-A-G			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CGB2	protein_coding	protein_coding	ENST00000359342	3	1327

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0304	0.613	125568	0	10	125578	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.625	96	80.2	1.20	0.00000539	994
Missense in Polyphen		41	33.473	1.2249		453
Synonymous	-1.57	49	36.8	1.33	0.00000244	375
Loss of Function	0.206	2	2.34	0.855	9.89e-8	37

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000621	0.0000621
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000615	0.0000529
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;hormone-mediated signaling pathway;regulation of signaling receptor activity
• Cellular component: extracellular space;cytoplasm
• Molecular function: hormone activity