CHGB

chromogranin B, the group of Granins

Basic information

Region (hg38): 20:5911510-5925353

Previous symbols: [ "SCG1" ]

Links

ENSG00000089199 ∙ NCBI:1114 ∙ OMIM:118920 ∙ HGNC:1930 ∙ Uniprot:P05060 ∙ 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 CHGB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHGB 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				3	1	4
missense			37	1	6	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	37	4	8

Variants in CHGB

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

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

Position	Type	Phenotype	Significance	ClinVar
20-5911670-G-T		not specified	Uncertain significance (Feb 14, 2023)
20-5911680-C-A		not specified	Uncertain significance (Apr 01, 2024)
20-5916350-A-G		not specified	Uncertain significance (Jun 18, 2021)
20-5916838-A-G		not specified	Uncertain significance (Feb 13, 2023)
20-5916866-C-T		not specified	Uncertain significance (Jun 27, 2022)
20-5916874-A-G		not specified	Uncertain significance (Feb 23, 2023)
20-5916881-C-T		not specified	Uncertain significance (Dec 28, 2023)
20-5922423-G-A		CHGB-related disorder	Benign (Jun 05, 2019)
20-5922451-G-C		not specified	Uncertain significance (May 30, 2024)
20-5922495-G-C		CHGB-related disorder	Benign (May 28, 2019)
20-5922511-T-G		not specified	Uncertain significance (Oct 03, 2022)
20-5922520-G-A		not specified	Uncertain significance (Feb 07, 2023)
20-5922526-G-A		not specified	Uncertain significance (Apr 17, 2024)
20-5922544-G-C		not specified	Uncertain significance (Aug 16, 2022)
20-5922578-A-G		not specified	Uncertain significance (Oct 20, 2021)
20-5922586-G-C		not specified	Uncertain significance (Aug 04, 2023)
20-5922607-C-T		not specified	Uncertain significance (Sep 14, 2023)
20-5922648-G-C		not specified	Uncertain significance (Jun 05, 2024)
20-5922701-A-G		not specified	Uncertain significance (Aug 17, 2022)
20-5922719-G-A		not specified	Uncertain significance (Jan 03, 2024)
20-5922727-C-G		not specified	Uncertain significance (Feb 15, 2023)
20-5922833-A-G		CHGB-related disorder	Benign (Dec 02, 2019)
20-5922926-A-G		not specified	Uncertain significance (Jan 22, 2024)
20-5922964-G-A		not specified	Uncertain significance (Jun 17, 2022)
20-5922974-G-A		not specified	Uncertain significance (May 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHGB	protein_coding	protein_coding	ENST00000378961	5	13932

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.36e-7	0.995	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0840	358	363	0.988	0.0000191	4495
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000368	0.000365
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000437	0.000435
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000301	0.000299
Middle Eastern	0.000437	0.000435
South Asian	0.000327	0.000327
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.286

Intolerance Scores

• loftool: 0.848
• rvis_EVS: 1.94
• rvis_percentile_EVS: 97.51

Haploinsufficiency Scores

• pHI: 0.200
• hipred: N
• hipred_score: 0.123
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.871

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chgb
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: regulation of signaling receptor activity;post-translational protein modification;cellular protein metabolic process
• Cellular component: extracellular space;endoplasmic reticulum lumen;secretory granule
• Molecular function: hormone activity;protein binding