GNAT1

G protein subunit alpha transducin 1, the group of G protein subunits alpha, group i

Basic information

Region (hg38): 3:50191610-50197696

Links

ENSG00000114349 ∙ NCBI:2779 ∙ OMIM:139330 ∙ HGNC:4393 ∙ Uniprot:P11488 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital stationary night blindness (Supportive), mode of inheritance: AD
• congenital stationary night blindness autosomal dominant 3 (Definitive), mode of inheritance: AD
• congenital stationary night blindness 1G (Limited), mode of inheritance: AR
• congenital stationary night blindness autosomal dominant 3 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Night blindness, congenital stationary, autosomal dominant 3; Night blindness, congenital stationary, autosomal recessive, 1G	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	8673138; 22190596

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GNAT1 gene.

• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GNAT1 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	68	1	71
missense			124	2	1	127
nonsense	6	2				8
start loss			2			2
frameshift	3	1	2			6
inframe indel			5			5
splice donor/acceptor (+/-2bp)	1	2				3
splice region			7	9		16
non coding			25	41	17	83
Total	10	5	160	111	19

Highest pathogenic variant AF is 0.0000328

Variants in GNAT1

This is a list of pathogenic ClinVar variants found in the GNAT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-50191724-C-G		Congenital stationary night blindness autosomal dominant 3	Benign (Jan 12, 2018)
3-50191726-A-G			Uncertain significance (Jul 21, 2021)
3-50191728-G-C			Uncertain significance (Nov 22, 2022)
3-50191732-G-A			Uncertain significance (Feb 18, 2021)
3-50191732-GC-G		Retinitis pigmentosa	Pathogenic (Jun 23, 2019)
3-50191735-G-C			Uncertain significance (May 18, 2021)
3-50191740-C-T		Congenital stationary night blindness autosomal dominant 3	Likely benign (Mar 03, 2021)
3-50191741-A-G			Uncertain significance (Mar 05, 2020)
3-50191746-T-C			Likely benign (Aug 09, 2022)
3-50191746-TGAG-T			Uncertain significance (Oct 13, 2022)
3-50191758-C-T			Likely benign (Mar 25, 2021)
3-50191763-G-A		Congenital stationary night blindness autosomal dominant 3	Benign/Likely benign (Jun 13, 2023)
3-50191764-G-A		Congenital stationary night blindness autosomal dominant 3	Benign/Likely benign (Oct 22, 2023)
3-50191767-G-A			Likely benign (Feb 27, 2023)
3-50191770-G-A		GNAT1-related disorder	Likely benign (Aug 28, 2023)
3-50191775-AG-A			Pathogenic (Nov 22, 2021)
3-50191783-A-G			Uncertain significance (Apr 23, 2022)
3-50191785-A-G			Likely benign (Sep 12, 2022)
3-50191791-C-T		GNAT1-related disorder	Likely benign (Jan 01, 2024)
3-50191792-G-A			Uncertain significance (Jun 27, 2023)
3-50191807-C-T			Likely pathogenic (May 01, 2019)
3-50191808-G-A		Congenital stationary night blindness autosomal dominant 3	Conflicting classifications of pathogenicity (Aug 01, 2024)
3-50191808-G-T			Uncertain significance (Sep 19, 2023)
3-50191812-C-T			Likely benign (May 07, 2022)
3-50191813-G-A			Uncertain significance (Oct 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GNAT1	protein_coding	protein_coding	ENST00000232461	8	4905

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.85e-13	0.0220	125677	0	65	125742	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.719	198	229	0.866	0.0000157	2339
Missense in Polyphen		105	115.56	0.90865		1230
Synonymous	0.529	93	99.7	0.933	0.00000850	647
Loss of Function	-0.177	18	17.2	1.05	8.22e-7	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000991	0.000991
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000110	0.000109
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.000213	0.000211
Middle Eastern	0.000110	0.000109
South Asian	0.0000654	0.0000653
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as signal transducer for the rod photoreceptor RHO. Required for normal RHO-mediated light perception by the retina (PubMed:22190596). Guanine nucleotide-binding proteins (G proteins) function as transducers downstream of G protein-coupled receptors (GPCRs), such as the photoreceptor RHO. The alpha chain contains the guanine nucleotide binding site and alternates between an active, GTP-bound state and an inactive, GDP-bound state. Activated RHO promotes GDP release and GTP binding. Signaling is mediated via downstream effector proteins, such as cGMP-phosphodiesterase (By similarity). {ECO:0000250|UniProtKB:P04695, ECO:0000269|PubMed:22190596}.
• Disease: DISEASE: Night blindness, congenital stationary, autosomal dominant 3 (CSNBAD3) [MIM:610444]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. {ECO:0000269|PubMed:17584859, ECO:0000269|PubMed:8673138}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Night blindness, congenital stationary, 1G (CSNB1G) [MIM:616389]: An autosomal recessive form of congenital stationary night blindness, a non-progressive retinal disorder characterized by impaired night vision or in dim light, with good vision only on bright days. {ECO:0000269|PubMed:22190596}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Phototransduction - Homo sapiens (human);Signaling by GPCR;Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding;Signal Transduction;visual signal transduction;Metabolism of proteins;Chaperonin-mediated protein folding;Visual signal transduction: Rods;Protein folding;G-protein activation;PLC beta mediated events;G-protein mediated events;Opioid Signalling;G alpha (i) signalling events;Activation of the phototransduction cascade;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.186

Intolerance Scores

• loftool: 0.349
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.780
• hipred: Y
• hipred_score: 0.548
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.633

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gnat1
• Phenotype: taste/olfaction phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); pigmentation phenotype; vision/eye 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;signal transduction;adenylate cyclase-modulating G protein-coupled receptor signaling pathway;visual perception;phototransduction, visible light;cell population proliferation;response to light stimulus;response to light intensity;rhodopsin mediated signaling pathway;regulation of rhodopsin mediated signaling pathway;eye photoreceptor cell development;detection of light stimulus involved in visual perception;sensory perception of umami taste;positive regulation of cyclic-nucleotide phosphodiesterase activity;negative regulation of cyclic-nucleotide phosphodiesterase activity;retina development in camera-type eye;cellular response to electrical stimulus
• Cellular component: photoreceptor outer segment;photoreceptor inner segment;cytosol;heterotrimeric G-protein complex;plasma membrane;membrane;apical plasma membrane;photoreceptor connecting cilium;photoreceptor outer segment membrane;neuronal cell body;photoreceptor disc membrane
• Molecular function: acyl binding;G protein-coupled receptor binding;GTPase activity;GTP binding;GDP binding;protein kinase binding;G-protein beta/gamma-subunit complex binding;metal ion binding