CHGA

chromogranin A, the group of Granins|Neuropeptides

Basic information

Region (hg38): 14:92923150-92935285

Links

ENSG00000100604 ∙ NCBI:1113 ∙ OMIM:118910 ∙ HGNC:1929 ∙ Uniprot:P10645 ∙ 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 CHGA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHGA 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			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in CHGA

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

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

Position	Type	Phenotype	Significance	ClinVar
14-92924225-A-T		not specified	Uncertain significance (Dec 15, 2023)
14-92926650-C-T		not specified	Uncertain significance (Jul 06, 2021)
14-92927555-C-T		not specified	Uncertain significance (May 23, 2023)
14-92927609-G-A		not specified	Uncertain significance (Aug 17, 2022)
14-92929755-G-A		not specified	Likely benign (Jun 30, 2023)
14-92929773-T-C		not specified	Uncertain significance (Sep 27, 2021)
14-92929779-G-T		not specified	Uncertain significance (Jul 20, 2021)
14-92929795-G-A		not specified	Likely benign (Apr 20, 2024)
14-92929799-C-G		not specified	Uncertain significance (Jul 05, 2024)
14-92931374-G-T		not specified	Uncertain significance (May 28, 2024)
14-92931428-G-T		not specified	Uncertain significance (Apr 29, 2024)
14-92931462-C-G		not specified	Uncertain significance (May 04, 2022)
14-92931471-A-G		not specified	Uncertain significance (Mar 31, 2024)
14-92931498-G-C		not specified	Uncertain significance (Jun 22, 2023)
14-92931502-G-C		not specified	Uncertain significance (Apr 01, 2024)
14-92931547-G-C		not specified	Uncertain significance (Feb 21, 2024)
14-92931582-G-A		not specified	Uncertain significance (Nov 12, 2024)
14-92932417-G-C		not specified	Uncertain significance (Jun 23, 2021)
14-92932456-C-A		not specified	Uncertain significance (Oct 14, 2023)
14-92932460-C-A		not specified	Uncertain significance (Sep 10, 2024)
14-92932460-C-T		not specified	Uncertain significance (Dec 08, 2023)
14-92932481-A-C		not specified	Uncertain significance (Sep 12, 2023)
14-92932499-C-T		not specified	Uncertain significance (Mar 25, 2024)
14-92932519-G-A		not specified	Uncertain significance (Feb 06, 2024)
14-92932549-G-A		not specified	Uncertain significance (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHGA	protein_coding	protein_coding	ENST00000216492	8	12214

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0304	0.969	125726	1	20	125747	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.821	215	252	0.854	0.0000146	2918
Missense in Polyphen		65	75.834	0.85714		976
Synonymous	0.134	102	104	0.983	0.00000634	868
Loss of Function	3.11	7	23.2	0.302	0.00000132	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000183	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.0000487	0.0000462
European (Non-Finnish)	0.0000543	0.0000527
Middle Eastern	0.000110	0.000109
South Asian	0.000242	0.000196
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pancreastatin: Strongly inhibits glucose induced insulin release from the pancreas.; FUNCTION: Serpinin: Regulates granule biogenesis in endocrine cells by up-regulating the transcription of protease nexin 1 (SERPINE2) via a cAMP-PKA-SP1 pathway. This leads to inhibition of granule protein degradation in the Golgi complex which in turn promotes granule formation. {ECO:0000250|UniProtKB:P26339}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.487

Intolerance Scores

• loftool: 0.669
• rvis_EVS: 2.11
• rvis_percentile_EVS: 97.88

Haploinsufficiency Scores

• pHI: 0.492
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.828

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chga
• Phenotype: renal/urinary system 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of the force of heart contraction;mast cell chemotaxis;organelle organization;regulation of blood pressure;antimicrobial humoral response;killing of cells of other organism;mast cell cytokine production;negative regulation of catecholamine secretion;mast cell degranulation;innate immune response;mast cell activation;negative regulation of insulin secretion;negative regulation of hormone secretion;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;defense response to fungus;positive regulation of cardiac muscle contraction;adenylate cyclase-activating adrenergic receptor signaling pathway involved in cardiac muscle relaxation;negative regulation of blood vessel diameter;positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway;negative regulation of neuron death;positive regulation of relaxation of cardiac muscle;positive regulation of dense core granule biogenesis
• Cellular component: extracellular region;extracellular space;secretory granule;transport vesicle membrane;chromaffin granule;mast cell granule;perinuclear region of cytoplasm