CHGB

protein-coding

chromogranin B, the group of Granins

Gene summary

This gene encodes a tyrosine-sulfated secretory protein abundant in peptidergic endocrine cells and neurons. This protein may serve as a precursor for regulatory peptides. [provided by RefSeq, Jan 2009]

Previous symbols:

SCG1

MANE transcript

NM_001819.3

Inheritance

—

ClinVar variants

U:100B:12

Top phenotype

CHGB-related disorder

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr20:5,911,510-5,925,353

External References & Databases

Ensembl (ENSG00000089199)

Transcript & Mutation Effects

hg38 • Region Span ~13.8 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 CHGB variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 100

CHGB-related disorderTotal: 10

not providedTotal: 3

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001819.3. 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				3 clinvar	1 clinvar	4
missense			100 clinvar	3 clinvar	5 clinvar	108
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	100	6	6	112

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001819.3	RefSeq	NP_001810.2	5	MANE Select
ENST00000378961.9	Ensembl	ENSP00000368244.4	5	MANE Select
ENST00000455042.1	Ensembl	ENSP00000416643.1	3	Standard
ENST00000886261.1	Ensembl	ENSP00000556320.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein phosphorylation
Post-translational protein modification
Metabolism of proteins
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)

Biological Process

regulation of signaling receptor activity
post-translational protein modification
cellular protein metabolic process

Molecular Function

hormone activity
protein binding

Cellular Component

extracellular space
endoplasmic reticulum lumen
secretory granule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378961
Coding exons: 5
Length: 13932
Individuals with no LoFs: 125682
Homozygous LoFs: 0
Heterozygous LoFs: 66
Defined: 125748
p: 0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0840	358	363	0.988	0.0000191	4495
Missense (PolyPhen)		110	117.76	0.93407		1636
Synonymous	-0.701	152	141	1.07	0.00000828	1182
Loss of Function	2.54	16	31.3	0.511	0.00000182	374

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00044	0.00044	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00030	0.00030	rare
South Asian	0.00033	0.00033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Secretogranin-1 is a neuroendocrine secretory granule protein, which may be the precursor for other biologically active peptides.;

Recessive Scores

pRec: 0.286

Intolerance Scores

LoFtool: 0.848
RVIS EVS: 1.94
RVIS percentile EVS: 97.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.871

Gene Damage Prediction

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