CGB1

chorionic gonadotropin subunit beta 1, the group of Glycoprotein hormone subunits

Basic information

Region (hg38): 19:49035568-49036895

Links

ENSG00000267631 ∙ NCBI:114335 ∙ OMIM:608823 ∙ HGNC:16721 ∙ Uniprot:A6NKQ9 ∙ 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 CGB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CGB1 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						0
missense			15	3		18
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	0

Variants in CGB1

This is a list of pathogenic ClinVar variants found in the CGB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49035626-C-G		not specified	Uncertain significance (Apr 10, 2023)
19-49035626-C-T		not specified	Uncertain significance (Sep 12, 2023)
19-49035642-G-A		not specified	Uncertain significance (Aug 17, 2021)
19-49035643-G-C		not specified	Uncertain significance (Aug 02, 2021)
19-49035648-G-C		not specified	Uncertain significance (Jan 18, 2023)
19-49035648-G-T		not specified	Uncertain significance (Mar 16, 2024)
19-49035656-G-A		not specified	Uncertain significance (Jan 29, 2024)
19-49035756-A-G		not specified	Uncertain significance (Dec 21, 2022)
19-49035795-T-C		not specified	Likely benign (Mar 08, 2024)
19-49035797-A-C		not specified	Uncertain significance (Jan 04, 2024)
19-49035798-C-G		not specified	Uncertain significance (Sep 17, 2021)
19-49035831-C-G		not specified	Uncertain significance (Jul 09, 2021)
19-49035836-C-G		not specified	Uncertain significance (Apr 24, 2024)
19-49035851-T-G		not specified	Likely benign (Apr 28, 2022)
19-49035873-C-G			Likely benign (Nov 01, 2022)
19-49035893-A-C		not specified	Uncertain significance (Apr 25, 2023)
19-49036137-A-G		not specified	Uncertain significance (Oct 27, 2023)
19-49036165-T-G		not specified	Uncertain significance (Apr 25, 2023)
19-49036189-G-C		not specified	Uncertain significance (Jan 22, 2024)
19-49036261-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CGB1	protein_coding	protein_coding	ENST00000301407	3	13176

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0363	0.647	125580	0	2	125582	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.859	128	103	1.24	0.00000725	959
Missense in Polyphen		43	37.337	1.1517		359
Synonymous	-1.10	55	45.6	1.21	0.00000318	348
Loss of Function	0.379	2	2.67	0.750	1.12e-7	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.430
• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.45

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.381

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