CGA
glycoprotein hormones, alpha polypeptide, the group of Receptor ligands|Glycoprotein hormone subunits
Basic information
Region (hg38): 6:87085498-87095106
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CGA 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 | 2 | |||||
| missense | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 0 | 1 | 1 |
Variants in CGA
This is a list of pathogenic ClinVar variants found in the CGA region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-87085839-G-A | Benign (Jul 30, 2018) | |||
| 6-87086295-G-A | Benign (May 15, 2018) | |||
| 6-87086328-T-C | Likely benign (May 11, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CGA | protein_coding | protein_coding | ENST00000369582 | 3 | 9609 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.345 | 0.603 | 117574 | 0 | 1 | 117575 | 0.00000425 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.50 | 30 | 63.7 | 0.471 | 0.00000333 | 754 |
| Missense in Polyphen | 9 | 31.457 | 0.28611 | 389 | ||
| Synonymous | 0.0978 | 27 | 27.7 | 0.976 | 0.00000187 | 218 |
| Loss of Function | 1.52 | 1 | 4.47 | 0.224 | 1.87e-7 | 64 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000939 | 0.00000939 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Shared alpha chain of the active heterodimeric glycoprotein hormones thyrotropin/thyroid stimulating hormone/TSH, lutropin/luteinizing hormone/LH, follitropin/follicle stimulating hormone/FSH and choriogonadotropin/CG. These hormones bind specific receptors on target cells that in turn activate downstream signaling pathways. {ECO:0000269|PubMed:24692546, ECO:0000269|PubMed:2494176}.;
- Pathway
- Regulation of lipolysis in adipocytes - Homo sapiens (human);Thyroid hormone synthesis - Homo sapiens (human);Autoimmune thyroid disease - Homo sapiens (human);GnRH signaling pathway - Homo sapiens (human);Prolactin signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);Intracellular Signalling Through LHCGR Receptor and Luteinizing Hormone/Choriogonadotropin;Intracellular Signalling Through FSH Receptor and Follicle Stimulating Hormone;Thyroxine (Thyroid Hormone) Production;Human Thyroid Stimulating Hormone (TSH) signaling pathway;Follicle Stimulating Hormone (FSH) signaling pathway;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors;Signaling by GPCR;Signal Transduction;Gene expression (Transcription);Peptide hormone metabolism;Generic Transcription Pathway;Metabolism of lipids;Post-translational protein modification;Reactions specific to the complex N-glycan synthesis pathway;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;GPCR signaling-G alpha q;Metabolism of amino acids and derivatives;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;RNA Polymerase II Transcription;Metabolism;G alpha (s) signalling events;Mineralocorticoid biosynthesis;Hormone ligand-binding receptors;Androgen biosynthesis;Metabolism of steroid hormones;Metabolism of steroids;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Glucocorticoid receptor regulatory network;TFAP2 (AP-2) family regulates transcription of growth factors and their receptors;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors;GPCR signaling-G alpha i;TSH;Thyroxine biosynthesis;Amine-derived hormones;Glycoprotein hormones;GPCR downstream signalling;Steroid hormones;Peptide hormone biosynthesis;FSH
(Consensus)
Recessive Scores
- pRec
- 0.405
Intolerance Scores
- loftool
- 0.187
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.39
Haploinsufficiency Scores
- pHI
- 0.00193
- hipred
- N
- hipred_score
- 0.286
- ghis
- 0.497
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0338
Mouse Genome Informatics
- Gene name
- Cga
- Phenotype
- homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland 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); reproductive system phenotype;
Zebrafish Information Network
- Gene name
- cga
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- orientation
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;G protein-coupled receptor signaling pathway;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of steroid biosynthetic process;peptide hormone processing;positive regulation of cell migration;positive regulation of transcription by RNA polymerase II
- Cellular component
- extracellular region;extracellular space;Golgi lumen;follicle-stimulating hormone complex
- Molecular function
- hormone activity;protein binding;follicle-stimulating hormone activity