GNGT1
G protein subunit gamma transducin 1, the group of G protein subunits gamma
Basic information
Region (hg38): 7:93591572-93911265
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GNGT1 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 | 1 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 1 | 0 | 0 |
Variants in GNGT1
This is a list of pathogenic ClinVar variants found in the GNGT1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-93886837-G-A | not specified | Uncertain significance (Feb 16, 2023) | ||
| 7-93886846-G-A | Benign (Apr 16, 2018) | |||
| 7-93886872-G-A | not specified | Uncertain significance (Dec 12, 2023) | ||
| 7-93887327-T-C | not specified | Uncertain significance (Sep 16, 2021) | ||
| 7-93889100-C-T | Likely benign (May 24, 2018) | |||
| 7-93889120-G-T | not specified | Uncertain significance (Jan 26, 2022) | ||
| 7-93889142-C-G | not specified | Uncertain significance (Mar 01, 2024) | ||
| 7-93889157-T-A | not specified | Uncertain significance (Jan 02, 2024) | ||
| 7-93890129-G-A | Benign (May 24, 2018) | |||
| 7-93890140-C-T | not specified | Uncertain significance (Jun 28, 2022) | ||
| 7-93890146-T-G | Benign (May 24, 2018) | |||
| 7-93890175-G-C | not specified | Uncertain significance (Jul 06, 2021) | ||
| 7-93890612-C-T | not specified | Uncertain significance (Jan 02, 2024) | ||
| 7-93890650-G-C | not specified | Uncertain significance (Jul 25, 2023) | ||
| 7-93906843-G-A | Malignant tumor of prostate | Uncertain significance (-) | ||
| 7-93910860-G-T | not specified | Uncertain significance (Jul 06, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GNGT1 | protein_coding | protein_coding | ENST00000248572 | 2 | 319693 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.253 | 0.650 | 125625 | 0 | 7 | 125632 | 0.0000279 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.619 | 47 | 36.5 | 1.29 | 0.00000167 | 478 |
| Missense in Polyphen | 12 | 10.558 | 1.1366 | 152 | ||
| Synonymous | -0.617 | 17 | 14.1 | 1.21 | 7.60e-7 | 129 |
| Loss of Function | 1.22 | 1 | 3.44 | 0.291 | 2.42e-7 | 39 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000153 | 0.000152 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000585 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000268 | 0.0000264 |
| Middle Eastern | 0.0000585 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Guanine nucleotide-binding proteins (G proteins) are involved as a modulator or transducer in various transmembrane signaling systems. The beta and gamma chains are required for the GTPase activity, for replacement of GDP by GTP, and for G protein- effector interaction.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Relaxin signaling pathway - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Retrograde endocannabinoid signaling - Homo sapiens (human);GABAergic synapse - Homo sapiens (human);Serotonergic synapse - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Circadian entrainment - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Cholinergic synapse - Homo sapiens (human);Phototransduction - Homo sapiens (human);Morphine addiction - Homo sapiens (human);Alcoholism - Homo sapiens (human);Myometrial Relaxation and Contraction Pathways;G Protein Signaling Pathways;Chemokine signaling pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Ras Signaling;Calcium Regulation in the Cardiac Cell;Estrogen signaling pathway;Signaling by GPCR;Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding;Signaling by WNT;Signal Transduction;bioactive peptide induced signaling pathway;g-protein signaling through tubby proteins;role of egf receptor transactivation by gpcrs in cardiac hypertrophy;aspirin blocks signaling pathway involved in platelet activation;regulation of ck1/cdk5 by type 1 glutamate receptors;cxcr4 signaling pathway;corticosteroids and cardioprotection;phospholipids as signalling intermediaries;cystic fibrosis transmembrane conductance regulator (cftr) and beta 2 adrenergic receptor (b2ar) pathway;ion channels and their functional role in vascular endothelium;ccr3 signaling in eosinophils;activation of csk by camp-dependent protein kinase inhibits signaling through the t cell receptor;pkc-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase;chrebp regulation by carbohydrates and camp;signaling pathway from g-protein families;thrombin signaling and protease-activated receptors;how progesterone initiates the oocyte maturation;attenuation of gpcr signaling;role of -arrestins in the activation and targeting of map kinases;activation of camp-dependent protein kinase pka;Thromboxane signalling through TP receptor;Metabolism of proteins;ADP signalling through P2Y purinoceptor 12;Chaperonin-mediated protein folding;Metabolism;Olfactory Signaling Pathway;G alpha (s) signalling events;Presynaptic function of Kainate receptors;Activation of kainate receptors upon glutamate binding;Adrenaline,noradrenaline inhibits insulin secretion;Transport of small molecules;Glucagon-like Peptide-1 (GLP1) regulates insulin secretion;Regulation of insulin secretion;Signal amplification;Neuronal System;roles of arrestin dependent recruitment of src kinases in gpcr signaling;Thrombin signalling through proteinase activated receptors (PARs);regulation of spermatogenesis by crem;actions of nitric oxide in the heart;Glucagon-type ligand receptors;Class B/2 (Secretin family receptors);GPCR ligand binding;Platelet activation, signaling and aggregation;Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits;Activation of GABAB receptors;Ca2+ pathway;Beta-catenin independent WNT signaling;ADP signalling through P2Y purinoceptor 1;fmlp induced chemokine gene expression in hmc-1 cells;Hemostasis;-arrestins in gpcr desensitization;Visual signal transduction: Rods;Protein folding;G-protein activation;GABA B receptor activation;GABA receptor activation;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses;Opioid Signalling;G alpha (i) signalling events;Activation of the phototransduction cascade;G alpha (12/13) signalling events;G alpha (z) signalling events;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;Vasopressin regulates renal water homeostasis via Aquaporins;Aquaporin-mediated transport;Activation of G protein gated Potassium channels;G beta:gamma signalling through PLC beta;Prostacyclin signalling through prostacyclin receptor;Integration of energy metabolism;Platelet homeostasis;G alpha (q) signalling events;G beta:gamma signalling through PI3Kgamma;G-protein beta:gamma signalling;GPCR downstream signalling;G protein gated Potassium channels;Inwardly rectifying K+ channels;Potassium Channels
(Consensus)
Recessive Scores
- pRec
- 0.178
Intolerance Scores
- loftool
- 0.283
- rvis_EVS
- 0.19
- rvis_percentile_EVS
- 66.57
Haploinsufficiency Scores
- pHI
- 0.749
- hipred
- Y
- hipred_score
- 0.621
- ghis
- 0.403
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Low | Medium |
Mouse Genome Informatics
- Gene name
- Gngt1
- 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); vision/eye phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- signal transduction;phototransduction;protein localization;cardiac muscle cell apoptotic process;rhodopsin mediated signaling pathway;eye photoreceptor cell development;cellular response to hypoxia
- Cellular component
- photoreceptor outer segment;photoreceptor inner segment;heterotrimeric G-protein complex;plasma membrane;photoreceptor disc membrane
- Molecular function
- GTPase activity;protein binding