GNAT3

G protein subunit alpha transducin 3, the group of G protein subunits alpha, group i

Basic information

Region (hg38): 7:80458634-80512064

Links

ENSG00000214415 ∙ NCBI:346562 ∙ OMIM:139395 ∙ HGNC:22800 ∙ Uniprot:A8MTJ3 ∙ 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 GNAT3 gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GNAT3 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in GNAT3

This is a list of pathogenic ClinVar variants found in the GNAT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-80458676-A-C		not specified	Uncertain significance (Jul 14, 2021)
7-80458698-C-G		not specified	Uncertain significance (Dec 18, 2023)
7-80458742-C-T		not specified	Uncertain significance (Jan 07, 2022)
7-80458807-A-C		not specified	Uncertain significance (Jun 28, 2023)
7-80458810-T-C		not specified	Uncertain significance (Jan 09, 2024)
7-80458838-C-T		not specified	Uncertain significance (Oct 14, 2021)
7-80462205-T-G		not specified	Uncertain significance (Oct 27, 2023)
7-80462248-G-A		not specified	Uncertain significance (Jan 04, 2024)
7-80462257-A-G		not specified	Uncertain significance (Apr 18, 2023)
7-80462510-C-T		not specified	Uncertain significance (Nov 18, 2022)
7-80462526-C-A		not specified	Uncertain significance (Oct 25, 2022)
7-80474259-C-A		not specified	Uncertain significance (Dec 03, 2021)
7-80474332-T-C		not specified	Uncertain significance (Jul 25, 2023)
7-80474333-T-C		not specified	Uncertain significance (Feb 12, 2024)
7-80478905-C-T		not specified	Uncertain significance (Jul 06, 2021)
7-80488539-C-A		not specified	Uncertain significance (Feb 10, 2023)
7-80488590-G-A		not specified	Uncertain significance (Apr 15, 2022)
7-80488617-T-G		not specified	Uncertain significance (Mar 21, 2022)
7-80488647-T-G		not specified	Uncertain significance (Feb 27, 2024)
7-80494626-C-G		not specified	Uncertain significance (Feb 28, 2023)
7-80511814-A-T		not specified	Uncertain significance (Dec 15, 2023)
7-80511883-C-A		not specified	Uncertain significance (Jun 02, 2023)
7-80511900-G-C		not specified	Uncertain significance (Oct 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GNAT3	protein_coding	protein_coding	ENST00000398291	8	53350

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000163	0.880	124838	1	94	124933	0.000380

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.257	157	166	0.944	0.00000776	2328
Missense in Polyphen		62	70.714	0.87677		1034
Synonymous	0.0858	58	58.8	0.986	0.00000285	624
Loss of Function	1.49	10	16.5	0.605	8.70e-7	227

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000357	0.000349
Ashkenazi Jewish	0.00	0.00
East Asian	0.000285	0.000276
Finnish	0.00	0.00
European (Non-Finnish)	0.000674	0.000627
Middle Eastern	0.000285	0.000276
South Asian	0.000302	0.000261
Other	0.000701	0.000659

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide-binding protein (G protein) alpha subunit playing a prominent role in bitter and sweet taste transduction as well as in umami (monosodium glutamate, monopotassium glutamate, and inosine monophosphate) taste transduction. Transduction by this alpha subunit involves coupling of specific cell-surface receptors with a cGMP-phosphodiesterase; Activation of phosphodiesterase lowers intracellular levels of cAMP and cGMP which may open a cyclic nucleotide-suppressible cation channel leading to influx of calcium, ultimately leading to release of neurotransmitter. Indeed, denatonium and strychnine induce transient reduction in cAMP and cGMP in taste tissue, whereas this decrease is inhibited by GNAT3 antibody. Gustducin heterotrimer transduces response to bitter and sweet compounds via regulation of phosphodiesterase for alpha subunit, as well as via activation of phospholipase C for beta and gamma subunits, with ultimate increase inositol trisphosphate and increase of intracellular Calcium. GNAT3 can functionally couple to taste receptors to transmit intracellular signal: receptor heterodimer TAS1R2/TAS1R3 senses sweetness and TAS1R1/TAS1R3 transduces umami taste, whereas the T2R family GPCRs act as bitter sensors. Functions also as lumenal sugar sensors in the gut to control the expression of the Na+-glucose transporter SGLT1 in response to dietaty sugar, as well as the secretion of Glucagon-like peptide- 1, GLP-1 and glucose-dependent insulinotropic polypeptide, GIP. Thus, may modulate the gut capacity to absorb sugars, with implications in malabsorption syndromes and diet-related disorders including diabetes and obesity. {ECO:0000269|PubMed:11917125, ECO:0000269|PubMed:17724330}.
• Pathway: Carbohydrate digestion and absorption - Homo sapiens (human);Taste transduction - Homo sapiens (human);Signaling by GPCR;Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding;Signal Transduction;Metabolism of proteins;ADP signalling through P2Y purinoceptor 12;Chaperonin-mediated protein folding;G alpha (s) signalling events;Signal amplification;Neuronal System;Platelet activation, signaling and aggregation;Adenylate cyclase inhibitory pathway;Inhibition of adenylate cyclase pathway;Activation of GABAB receptors;Hemostasis;Protein folding;G-protein activation;GABA B receptor activation;PLC beta mediated events;GABA receptor activation;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses;G-protein mediated events;Opioid Signalling;G alpha (i) signalling events;G alpha (z) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.431
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.296
• hipred: N
• hipred_score: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.677

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gnat3
• Phenotype: taste/olfaction 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)

Gene ontology

• Biological process: detection of chemical stimulus involved in sensory perception of bitter taste;protein folding;G protein-coupled receptor signaling pathway;adenylate cyclase-modulating G protein-coupled receptor signaling pathway;adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;response to nicotine;sensory perception of sweet taste;sensory perception of umami taste
• Cellular component: acrosomal vesicle;photoreceptor outer segment;photoreceptor inner segment;heterotrimeric G-protein complex;plasma membrane;axoneme;apical plasma membrane;protein-containing complex
• Molecular function: G protein-coupled receptor binding;GTPase activity;GTP binding;G-protein beta/gamma-subunit complex binding;metal ion binding