CGB1

protein-coding

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

Gene summary

The beta subunit of chorionic gonadotropin (CGB) is encoded by six highly homologous and structurally similar genes that are arranged in tandem and inverted pairs on chromosome 19q13.3, and contiguous with the luteinizing hormone beta (LHB) subunit gene. The CGB genes are primarily distinguished by differences in the 5' untranscribed region. This gene was originally thought to be one of the two pseudogenes (CGB1 and CGB2) of CGB subunit, however, detection of CGB1 and CGB2 transcripts in vivo, and their presence on the polysomes, suggested that these transcripts are translated. To date, a protein product corresponding to CGB1 has not been isolated. The deduced sequence of the hypothetical protein of 132 aa does not share any similarity with that of functional CGB subunits (PMID:8954017). However, a 155 aa protein, translated from a different frame, is about the same size, and shares 98% identity with other CGB subunits. [provided by RefSeq, Jul 2008]

MANE transcript

NM_033377.2

Inheritance

—

ClinVar variants

U:41B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr19:49,035,569-49,036,895

External References & Databases

Ensembl (ENSG00000267631)

Transcript & Mutation Effects

hg38 • Region Span ~1.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CGB1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 45

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033377.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			41 clinvar	4 clinvar		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	6	0	47

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033377.2	RefSeq	NP_203695.2	3	MANE Select
ENST00000301407.8	Ensembl	ENSP00000301407.6	3	MANE Select
NM_001382421.1	RefSeq	NP_001369350.1	2	Standard
ENST00000601167.1	Ensembl	ENSP00000472896.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

G protein-coupled receptor signaling pathway
hormone-mediated signaling pathway
regulation of signaling receptor activity

Molecular Function

hormone activity

Cellular Component

extracellular space
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000301407
Coding exons: 3
Length: 13176
Individuals with no LoFs: 125580
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125582
p: 0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.859	128	103	1.24	0.00000725	959
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.430
RVIS EVS: 0.59
RVIS percentile EVS: 82.45

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.381

Gene Damage Prediction

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