CHGA
chromogranin A, the group of Granins|Neuropeptides
Basic information
Region (hg38): 14:92923150-92935285
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (50 variants)
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. These statistics are base on transcript: NM_000001275.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 45 | 50 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 45 | 5 | 0 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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
- ghis
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
- Molecular function