GNAT2 (G protein subunit alpha transducin 2)

Gene

• Entrez ID: 2780
• Gene name: G protein subunit alpha transducin 2
• Gene symbol: GNAT2
• Synonyms (NCBI Gene): ACHM4, GNATC, HG1D
• Chromosome: 1
• Chromosome location: 1p13.3
• Summary: Transducin is a 3-subunit guanine nucleotide-binding protein (G protein) which stimulates the coupling of rhodopsin and cGMP-phoshodiesterase during visual impulses. The transducin alpha subunits in rods and cones are encoded by separate genes. This gene

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121434585	G>A	Pathogenic	Stop gained, coding sequence variant
rs146606352	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs397515384	C>T	Conflicting-interpretations-of-pathogenicity	Intron variant
rs745308973	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs748981899	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs1240543072	A>C,T	Likely-pathogenic	Missense variant, coding sequence variant
rs1268228697	CTT>-	Likely-pathogenic	Inframe deletion, coding sequence variant
rs1403825722	G>A	Pathogenic	Coding sequence variant, stop gained
rs1553226355	G>T	Likely-pathogenic	Coding sequence variant, stop gained
rs1553226581	C>G	Likely-pathogenic	Intron variant
rs1557917535	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs1557917899	->TTGA	Pathogenic	Coding sequence variant, frameshift variant
rs1557918544	A>G	Pathogenic	Splice donor variant
rs1557918638	T>G	Pathogenic	Splice acceptor variant
rs1557918911	->A	Pathogenic	Coding sequence variant, frameshift variant
rs1557920291	TTCAGCA>ATACAG	Pathogenic	Coding sequence variant, frameshift variant
rs1570562309	C>T	Pathogenic	Coding sequence variant, missense variant
rs1570565168	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT021422	hsa-miR-9-5p	Microarray	17612493
MIRT023994	hsa-miR-1-3p	Proteomics;Microarray	18668037

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000902	Process	Cell morphogenesis	IEA
GO:0001580	Process	Detection of chemical stimulus involved in sensory perception of bitter taste	IBA
GO:0001580	Process	Detection of chemical stimulus involved in sensory perception of bitter taste	IEA
GO:0001664	Function	G protein-coupled receptor binding	IBA
GO:0001750	Component	Photoreceptor outer segment	IBA
GO:0001750	Component	Photoreceptor outer segment	IDA	2534964
GO:0001750	Component	Photoreceptor outer segment	IEA
GO:0001750	Component	Photoreceptor outer segment	ISS
GO:0001917	Component	Photoreceptor inner segment	IBA
GO:0001917	Component	Photoreceptor inner segment	IDA	2534964
GO:0001917	Component	Photoreceptor inner segment	IEA
GO:0003924	Function	GTPase activity	IBA
GO:0003924	Function	GTPase activity	IEA
GO:0005525	Function	GTP binding	IEA
GO:0005525	Function	GTP binding	NAS	1936270
GO:0005737	Component	Cytoplasm	IBA
GO:0005834	Component	Heterotrimeric G-protein complex	IBA
GO:0005834	Component	Heterotrimeric G-protein complex	NAS	1936270, 2534964
GO:0005886	Component	Plasma membrane	TAS
GO:0007165	Process	Signal transduction	IEA
GO:0007186	Process	G protein-coupled receptor signaling pathway	IEA
GO:0007186	Process	G protein-coupled receptor signaling pathway	NAS	2534964
GO:0007188	Process	Adenylate cyclase-modulating G protein-coupled receptor signaling pathway	IBA
GO:0007188	Process	Adenylate cyclase-modulating G protein-coupled receptor signaling pathway	IEA
GO:0007204	Process	Positive regulation of cytosolic calcium ion concentration	IEA
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	NAS	2534964
GO:0007602	Process	Phototransduction	IEA
GO:0007602	Process	Phototransduction	NAS	2534964
GO:0007632	Process	Visual behavior	IEA
GO:0008020	Function	G protein-coupled photoreceptor activity	NAS	2534964
GO:0008104	Process	Intracellular protein localization	IEA
GO:0009411	Process	Response to UV	IEA
GO:0009416	Process	Response to light stimulus	IEA
GO:0009583	Process	Detection of light stimulus	IEA
GO:0009584	Process	Detection of visible light	IEA
GO:0009642	Process	Response to light intensity	IEA
GO:0009642	Process	Response to light intensity	IEA
GO:0010467	Process	Gene expression	IEA
GO:0016020	Component	Membrane	IEA
GO:0019001	Function	Guanyl nucleotide binding	IEA
GO:0031683	Function	G-protein beta/gamma-subunit complex binding	IBA
GO:0031683	Function	G-protein beta/gamma-subunit complex binding	IEA
GO:0042417	Process	Dopamine metabolic process	IEA
GO:0042622	Component	Photoreceptor outer segment membrane	ISS
GO:0042670	Process	Retinal cone cell differentiation	IEA
GO:0042995	Component	Cell projection	IEA
GO:0043010	Process	Camera-type eye development	IEA
GO:0045202	Component	Synapse	IEA
GO:0046549	Process	Retinal cone cell development	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0048771	Process	Tissue remodeling	IEA
GO:0048877	Process	Homeostasis of number of retina cells	IEA
GO:0050908	Process	Detection of light stimulus involved in visual perception	IEA
GO:0050908	Process	Detection of light stimulus involved in visual perception	IMP	12077706
GO:0051938	Process	L-glutamate import	IEA
GO:0060221	Process	Retinal rod cell differentiation	IEA
GO:0097719	Process	Neural tissue regeneration	IEA
GO:0120302	Process	Background adaptation	IEA
GO:0150103	Process	Reactive gliosis	IEA
GO:1904390	Process	Cone retinal bipolar cell differentiation	IEA

Other IDs

• MIM: 139340
• HGNC: 4394
• e!Ensembl: ENSG00000134183

Protein

• UniProt ID: P19087
• Protein name: Guanine nucleotide-binding protein G(t) subunit alpha-2 (Transducin alpha-2 chain)
• Protein function: Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems. Transducin is an amplifier and one of the transducers of a visual impulse that performs the coupling between r
• PDB: 6N84, 6N85
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00503	G-alpha	13 → 343	G-protein alpha subunit	Domain

• Tissue specificity: TISSUE SPECIFICITY: Retinal rod outer segment.
• Sequence:

  MGSGASAEDKELAKRSKELEKKLQEDADKEAKTVKLLLLGAGESGKSTIVKQMKIIHQDG
  YSPEECLEFKAIIYGNVLQSILAIIRAMTTLGIDYAEPSCADDGRQLNNLADSIEEGTMP
  PELVEVIRRLWKDGGVQACFERAAEYQLNDSASYYLNQLERITDPEYLPSEQDVLRSRVK
  TTGIIETKFSVKDLNFRMFDVGGQRSERKKWIHCFEGVTCIIFCAALSAYDMVLVEDDEV
  NRMHESLHLFNSICNHKFFAATSIVLFLNKKDLFEEKIKKVHLSICFPEYDGNNSYDDAG
  NYIKSQFLDLNMRKDVKEIYSHMTCATDTQNVKFVFDAVTDIIIKENLKDCGLF

• Sequence length: 354

Pathways

KEGG:

Phototransduction

Reactome:

PLC beta mediated events
G-protein activation
Ca2+ pathway
G alpha (i) signalling events
Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Abnormality of the eye	Likely pathogenic	rs1553226355	RCV000505046	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Achromatopsia	Pathogenic	rs745308973, rs1557918638	RCV003483692 RCV001199475	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Achromatopsia 4	Pathogenic; Likely pathogenic	rs121434585, rs2101121827, rs745308973, rs1557917535, rs748981899, rs1557917899, rs1557918619, rs1557918635, rs1557918911, rs1403825722, rs1557920291, rs146606352, rs1557918544, rs1557918638, rs1570562309	RCV000017273 RCV000017274 RCV000625933 RCV000761412 RCV000761410 RCV000761407 RCV000761403 RCV000761402 RCV000761400 RCV000761399 RCV000761396 RCV000761395 RCV000761405 RCV000761401 RCV001002705	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cone dystrophy	Pathogenic	rs1557918619	RCV001199818	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Pathogenic; Likely pathogenic	rs1234568897, rs1557918635, rs1557918544, rs1649583816	RCV004817095 RCV004817972 RCV001074059 RCV001073745	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
COLOR BLINDNESS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DEFECTS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GNAT2-related disorder	Conflicting classifications of pathogenicity; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBESITY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROGRESSIVE CONE DYSTROPHY	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Achromatopsia	Achromatopsia	BEFREE	12077706, 12205108, 15712225, 21107338, 24664760, 25277229, 27718025, 31058429, 31237654		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Achromatopsia	Achromatopsia	CTD_human_DG	12077706		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Achromatopsia	Achromatopsia	ORPHANET_DG	12077706		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Achromatopsia	Achromatopsia	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Achromatopsia	Achromatopsia	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Achromatopsia	Achromatopsia	GENOMICS_ENGLAND_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Achromatopsia	Achromatopsia	HPO_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Achromatopsia 3	Achromatopsia	Pubtator	32203983	Associate	★☆☆☆☆ Found in Text Mining only
ACHROMATOPSIA 4	Achromatopsia	CLINVAR_DG	12077706, 21107338		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
ACHROMATOPSIA 4	Achromatopsia	BEFREE	12205108		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
ACHROMATOPSIA 4	Achromatopsia	GENOMICS_ENGLAND_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
ACHROMATOPSIA 4	Achromatopsia	CTD_human_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Amaurosis congenita of Leber, type 1	Leber congenital amaurosis	BEFREE	29721936		★☆☆☆☆ Found in Text Mining only
Color blindness	Color Blindness	CTD_human_DG	12077706		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Color Blindness, Acquired	Color blindness	CTD_human_DG	12077706		★☆☆☆☆ Found in Text Mining only
Color Blindness, Blue	Color blindness	CTD_human_DG	12077706		★☆☆☆☆ Found in Text Mining only
Color Blindness, Inherited	Color blindness	CTD_human_DG	12077706		★☆☆☆☆ Found in Text Mining only
Color Blindness, Red	Color blindness	CTD_human_DG	12077706		★☆☆☆☆ Found in Text Mining only
Color Blindness, Red-Green	Color blindness	CTD_human_DG	12077706		★☆☆☆☆ Found in Text Mining only
Color Vision Defects	Color vision deficiency	Pubtator	12077706, 12205108, 18636117, 22901948, 25277229, 31237654, 32203983, 32913385, 34360608, 36980963, 37372476	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cone Dystrophy	Cone dystrophy	Pubtator	12205108, 14609822	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cone Dystrophy	Cone Dystrophy	BEFREE	14609822		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cone monochromatism	Cone monochromatism	BEFREE	12205108, 15557429		★☆☆☆☆ Found in Text Mining only
Cone monochromatism	Cone monochromatism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cone-Rod Dystrophies	Cone-rod dystrophy	BEFREE	15094710		★☆☆☆☆ Found in Text Mining only
Cone-Rod Dystrophy 2	Cone-rod dystrophy	BEFREE	15094710		★☆☆☆☆ Found in Text Mining only
Disorder of eye	Disorder Of Eye	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Dyschromatopsia	Dyschromatopsia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Exotropia	Exotropia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hyperopia	Hyperopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	Pubtator	36980963	Associate	★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus Pathologic	Nystagmus	Pubtator	14609822, 32203983	Associate	★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	GWASDB_DG	23563607		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obesity	Obesity	GWASCAT_DG	23563607		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obesity	Obesity	Pubtator	23563607	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pendular Nystagmus	Pendular nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Progressive Cone Dystrophy	Cone Dystrophy	BEFREE	12205108		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Progressive cone dystrophy	Cone Dystrophy	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Progressive cone dystrophy (without rod involvement)	Progressive Cone Dystrophy	ORPHANET_DG	14609822		★☆☆☆☆ Found in Text Mining only
Retinal cone dystrophy 2	Retinal Cone Dystrophy	BEFREE	23328348		★☆☆☆☆ Found in Text Mining only
Retinal Dystrophies	Retinal Dystrophy	BEFREE	12205108		★☆☆☆☆ Found in Text Mining only
Usher syndrome, type 1A	Usher Syndrome	BEFREE	8970808		★☆☆☆☆ Found in Text Mining only
Usher Syndrome, Type I	Usher Syndrome	BEFREE	8970808		★☆☆☆☆ Found in Text Mining only
Vision Disorders	Visual disorder	Pubtator	14609822, 32203983	Associate	★☆☆☆☆ Found in Text Mining only