GNA13
G protein subunit alpha 13
Basic information
Region (hg38): 17:65009289-65056740
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 GNA13 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 2 |
Variants in GNA13
This is a list of pathogenic ClinVar variants found in the GNA13 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-65014265-G-C | Neoplasm | - (-) | ||
| 17-65014282-T-C | not specified | Uncertain significance (Oct 20, 2021) | ||
| 17-65014290-C-T | Benign (Feb 16, 2018) | |||
| 17-65014362-G-C | Neoplasm | - (-) | ||
| 17-65014370-G-A | not specified | Uncertain significance (Jun 16, 2024) | ||
| 17-65014441-T-C | not specified | Uncertain significance (Feb 28, 2023) | ||
| 17-65014543-T-C | not specified | Uncertain significance (Mar 01, 2023) | ||
| 17-65014565-C-T | not specified | Uncertain significance (Jan 30, 2024) | ||
| 17-65053576-G-A | not specified | Uncertain significance (Jul 14, 2023) | ||
| 17-65053580-T-C | Benign (Feb 16, 2018) | |||
| 17-65053600-C-G | not specified | Uncertain significance (Apr 28, 2022) | ||
| 17-65053603-C-T | not specified | Uncertain significance (Feb 23, 2023) | ||
| 17-65053641-G-A | not specified | Uncertain significance (Dec 03, 2021) | ||
| 17-65056317-T-G | not specified | Uncertain significance (Oct 02, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GNA13 | protein_coding | protein_coding | ENST00000439174 | 4 | 46125 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.867 | 0.133 | 125743 | 0 | 2 | 125745 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.71 | 109 | 223 | 0.489 | 0.0000125 | 2493 |
| Missense in Polyphen | 42 | 107.52 | 0.39063 | 1160 | ||
| Synonymous | 0.989 | 74 | 85.6 | 0.864 | 0.00000456 | 724 |
| Loss of Function | 3.16 | 2 | 15.4 | 0.130 | 8.54e-7 | 171 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems (PubMed:15240885, PubMed:16787920, PubMed:16705036, PubMed:27084452). Activates effector molecule RhoA by binding and activating RhoGEFs (ARHGEF1/p115RhoGEF, ARHGEF11/PDZ-RhoGEF and ARHGEF12/LARG) (PubMed:15240885, PubMed:12515866). GNA13-dependent Rho signaling subsequently regulates transcription factor AP-1 (activating protein-1) (By similarity). Promotes tumor cell invasion and metastasis by activating RhoA/ROCK signaling pathway (PubMed:16787920, PubMed:16705036, PubMed:27084452). Inhibits CDH1-mediated cell adhesion in process independent from Rho activation (PubMed:11976333). {ECO:0000250|UniProtKB:P27601, ECO:0000269|PubMed:11976333, ECO:0000269|PubMed:12515866, ECO:0000269|PubMed:15240885, ECO:0000269|PubMed:16705036, ECO:0000269|PubMed:16787920, ECO:0000269|PubMed:27084452}.;
- Pathway
- Platelet activation - Homo sapiens (human);Long-term depression - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Platelet Aggregation Inhibitor Pathway, Pharmacodynamics;miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Human Thyroid Stimulating Hormone (TSH) signaling pathway;G Protein Signaling Pathways;Regulation of Actin Cytoskeleton;G13 Signaling Pathway;Signaling by GPCR;Signal Transduction;pkc-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase;thrombin signaling and protease-activated receptors;Thromboxane signalling through TP receptor;Rho GTPase cycle;Signal amplification;Thrombin signalling through proteinase activated receptors (PARs);Platelet activation, signaling and aggregation;Signaling by Rho GTPases;CXCR4-mediated signaling events;Hemostasis;NRAGE signals death through JNK;Thromboxane A2 receptor signaling;Posttranslational regulation of adherens junction stability and dissassembly;Death Receptor Signalling;p75 NTR receptor-mediated signalling;G alpha (12/13) signalling events;TSH;GPCR downstream signalling;PAR4-mediated thrombin signaling events;PAR1-mediated thrombin signaling events;LPA receptor mediated events;S1P3 pathway;S1P4 pathway;Cell death signalling via NRAGE, NRIF and NADE;Plasma membrane estrogen receptor signaling;Sphingosine 1-phosphate (S1P) pathway;S1P2 pathway
(Consensus)
Recessive Scores
- pRec
- 0.120
Intolerance Scores
- loftool
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 60.09
Haploinsufficiency Scores
- pHI
- 0.226
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.470
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.969
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gna13
- Phenotype
- embryo phenotype; hematopoietic system phenotype; 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); normal phenotype; 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); immune system phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); muscle phenotype;
Zebrafish Information Network
- Gene name
- gna13b
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- branching involved in blood vessel morphogenesis;in utero embryonic development;signal transduction;G protein-coupled receptor signaling pathway;adenylate cyclase-modulating G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;Rho protein signal transduction;regulation of cell shape;cell differentiation;platelet activation;regulation of cell migration;activation of phospholipase D activity;positive regulation of apoptotic process;regulation of small GTPase mediated signal transduction
- Cellular component
- nucleus;cytosol;heterotrimeric G-protein complex;plasma membrane;focal adhesion;membrane;brush border membrane;melanosome;extracellular exosome
- Molecular function
- G protein-coupled receptor binding;GTPase activity;guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;protein binding;GTP binding;G-protein beta/gamma-subunit complex binding;D5 dopamine receptor binding;metal ion binding