Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	1261
Gene name Gene Name - the full gene name approved by the HGNC.	Cyclic nucleotide gated channel subunit alpha 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	CNGA3
Synonyms (NCBI Gene) Gene synonyms aliases	ACHM2, CCNC1, CCNCa, CCNCalpha, CNCG3, CNG3
Chromosome Chromosome number	2
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	2q11.2
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a member of the cyclic nucleotide-gated cation channel protein family which is required for normal vision and olfactory signal transduction. Mutations in this gene are associated with achromatopsia (rod monochromacy) and color blindness.

Show/Hide all(53)

SNP ID	Visualize variation	Clinical significance	Consequence
rs62156348	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs104893612	C>T	Pathogenic	Coding sequence variant, missense variant
rs104893613	C>T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs104893614	G>A	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs104893615	G>A	Pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs104893616	C>G	Pathogenic	Coding sequence variant, missense variant
rs104893617	C>A,T	Pathogenic, likely-pathogenic	Coding sequence variant, synonymous variant, missense variant
rs104893619	G>A	Pathogenic	Coding sequence variant, missense variant
rs104893620	C>T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs104893621	C>T	Pathogenic	Coding sequence variant, missense variant
rs116448158	G>A	Likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs117522010	G>A,T	Likely-pathogenic	Coding sequence variant, missense variant
rs137852608	C>T	Pathogenic	Coding sequence variant, missense variant
rs138958917	C>G,T	Pathogenic	Coding sequence variant, missense variant
rs141386891	C>T	Pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs146195955	G>C	Likely-pathogenic, pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs147118493	G>A	Pathogenic, conflicting-interpretations-of-pathogenicity	Splice donor variant
rs147415641	G>A	Likely-benign, pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs148616345	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs149802213	C>A,G	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs199837807	G>A,C	Likely-pathogenic	Coding sequence variant, missense variant
rs374258471	G>A,C	Likely-pathogenic	Coding sequence variant, missense variant
rs375152706	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs552069173	G>A	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs749036398	ACTC>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs753625117	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs753692812	C>T	Likely-pathogenic	Coding sequence variant, stop gained
rs757470958	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs762773298	G>A,T	Pathogenic	Coding sequence variant, stop gained, missense variant
rs763041373	G>A	Pathogenic	Coding sequence variant, missense variant
rs774676415	G>A	Pathogenic	Missense variant, coding sequence variant
rs777509481	C>T	Pathogenic	Coding sequence variant, stop gained
rs777878533	ATC>-	Pathogenic-likely-pathogenic	Inframe deletion, coding sequence variant
rs778114016	G>A	Pathogenic	Missense variant, coding sequence variant
rs781227859	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs786205531	G>A,C	Likely-pathogenic	Coding sequence variant, missense variant
rs786205532	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1064797258	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs1330263985	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1464167194	C>G,T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs1553447991	G>C	Likely-pathogenic	Splice acceptor variant
rs1553450734	T>C	Pathogenic	Coding sequence variant, missense variant
rs1553450762	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1553450764	G>A	Pathogenic	Stop gained, coding sequence variant
rs1553450895	AA>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1553450979	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1558811557	->TCAGTGCTGCAGCCGGGGATCG	Pathogenic, likely-pathogenic	Frameshift variant, coding sequence variant
rs1558820134	G>T	Pathogenic	Coding sequence variant, missense variant
rs1558820471	TTA>AG	Pathogenic	Frameshift variant, coding sequence variant
rs1574385431	T>C	Pathogenic	Coding sequence variant, missense variant
rs1574390600	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1574390811	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1574391103	G>-	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all(42)

miRTarBase ID	miRNA	Experiments	Reference
MIRT561054	hsa-miR-3185	PAR-CLIP	20371350
MIRT561053	hsa-miR-1252-5p	PAR-CLIP	20371350
MIRT561052	hsa-miR-3611	PAR-CLIP	20371350
MIRT561054	hsa-miR-3185	PAR-CLIP	20371350
MIRT561053	hsa-miR-1252-5p	PAR-CLIP	20371350
MIRT561052	hsa-miR-3611	PAR-CLIP	20371350
MIRT561054	hsa-miR-3185	PAR-CLIP	20371350
MIRT561053	hsa-miR-1252-5p	PAR-CLIP	20371350
MIRT561052	hsa-miR-3611	PAR-CLIP	20371350
MIRT561054	hsa-miR-3185	PAR-CLIP	20371350
MIRT561053	hsa-miR-1252-5p	PAR-CLIP	20371350
MIRT561052	hsa-miR-3611	PAR-CLIP	20371350
MIRT899528	hsa-miR-1296	CLIP-seq
MIRT899529	hsa-miR-296-5p	CLIP-seq
MIRT899530	hsa-miR-4512	CLIP-seq
MIRT899531	hsa-miR-185	CLIP-seq
MIRT899532	hsa-miR-3150b-3p	CLIP-seq
MIRT899533	hsa-miR-3613-5p	CLIP-seq
MIRT899534	hsa-miR-4279	CLIP-seq
MIRT899535	hsa-miR-4306	CLIP-seq
MIRT899536	hsa-miR-4424	CLIP-seq
MIRT899537	hsa-miR-4644	CLIP-seq
MIRT899538	hsa-miR-4724-3p	CLIP-seq
MIRT899539	hsa-miR-4781-3p	CLIP-seq
MIRT899540	hsa-miR-4784	CLIP-seq
MIRT899541	hsa-miR-516a-3p	CLIP-seq
MIRT899542	hsa-miR-583	CLIP-seq
MIRT1966824	hsa-miR-1252	CLIP-seq
MIRT1966825	hsa-miR-1290	CLIP-seq
MIRT1966826	hsa-miR-27a	CLIP-seq
MIRT1966827	hsa-miR-27b	CLIP-seq
MIRT1966828	hsa-miR-3167	CLIP-seq
MIRT1966829	hsa-miR-3977	CLIP-seq
MIRT1966830	hsa-miR-4782-5p	CLIP-seq
MIRT1966831	hsa-miR-513a-5p	CLIP-seq
MIRT1966832	hsa-miR-876-5p	CLIP-seq
MIRT2447292	hsa-miR-3173-5p	CLIP-seq
MIRT2447293	hsa-miR-3200-3p	CLIP-seq
MIRT2447294	hsa-miR-4325	CLIP-seq
MIRT2447295	hsa-miR-450b-5p	CLIP-seq
MIRT2447296	hsa-miR-518a-5p	CLIP-seq
MIRT2447297	hsa-miR-527	CLIP-seq

Show/Hide all(46)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0005216	Function	Monoatomic ion channel activity	IEA
GO:0005221	Function	Intracellularly cyclic nucleotide-activated monoatomic cation channel activity	IEA
GO:0005222	Function	Intracellularly cAMP-activated cation channel activity	IBA
GO:0005222	Function	Intracellularly cAMP-activated cation channel activity	IDA	12815043
GO:0005223	Function	Intracellularly cGMP-activated cation channel activity	IBA
GO:0005223	Function	Intracellularly cGMP-activated cation channel activity	IDA	12815043
GO:0005223	Function	Intracellularly cGMP-activated cation channel activity	IEA
GO:0005223	Function	Intracellularly cGMP-activated cation channel activity	IMP	24164424
GO:0005262	Function	Calcium channel activity	IEA
GO:0005272	Function	Sodium channel activity	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA	12815043
GO:0005886	Component	Plasma membrane	IEA
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006812	Process	Monoatomic cation transport	IMP	24164424
GO:0006814	Process	Sodium ion transport	IEA
GO:0006816	Process	Calcium ion transport	IEA
GO:0007165	Process	Signal transduction	TAS	9517456
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	TAS	9662398
GO:0015276	Function	Ligand-gated monoatomic ion channel activity	TAS	9517456
GO:0016020	Component	Membrane	IEA
GO:0017022	Function	Myosin binding	IEA
GO:0017071	Component	Intracellular cyclic nucleotide activated cation channel complex	IBA
GO:0030425	Component	Dendrite	IEA
GO:0030553	Function	CGMP binding	IBA
GO:0030553	Function	CGMP binding	IDA	37463923
GO:0030553	Function	CGMP binding	IEA
GO:0030553	Function	CGMP binding	IMP	24164424
GO:0032026	Process	Response to magnesium ion	IEA
GO:0034220	Process	Monoatomic ion transmembrane transport	IEA
GO:0035725	Process	Sodium ion transmembrane transport	IEA
GO:0043025	Component	Neuronal cell body	IEA
GO:0043194	Component	Axon initial segment	IEA
GO:0043204	Component	Perikaryon	IEA
GO:0045296	Function	Cadherin binding	IEA
GO:0051591	Process	Response to cAMP	IEA
GO:0055085	Process	Transmembrane transport	IEA
GO:0060041	Process	Retina development in camera-type eye	IBA
GO:0070588	Process	Calcium ion transmembrane transport	IEA
GO:0097386	Component	Glial cell projection	IEA
GO:0098655	Process	Monoatomic cation transmembrane transport	IBA
GO:0098659	Process	Inorganic cation import across plasma membrane	IEA
GO:1902495	Component	Transmembrane transporter complex	IDA	24164424

MIM	HGNC	e!Ensembl
600053	2150	ENSG00000144191

Protein

UniProt ID

Q16281

Protein name

Cyclic nucleotide-gated channel alpha-3 (CNG channel alpha-3) (CNG-3) (CNG3) (Cone photoreceptor cGMP-gated channel subunit alpha-3)

Protein function

Pore-forming subunit of the cone cyclic nucleotide-gated channel. Mediates cone photoresponses at bright light converting transient changes in intracellular cGMP levels into electrical signals. In the dark, cGMP levels are high and keep the chan

PDB

3SWY , 7RHS , 8ETP , 8EU3 , 8EUC , 8EV8 , 8EV9 , 8EVA , 8EVB , 8EVC

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00520	Ion_trans	168 → 411	Ion transport protein	Family
PF00027	cNMP_binding	500 → 591	Cyclic nucleotide-binding domain	Domain
PF16526	CLZ	598 → 668	C-terminal leucine zipper domain of cyclic nucleotide-gated channels	Coiled-coil

Tissue specificity

TISSUE SPECIFICITY: Prominently expressed in retina.

Sequence

MAKINTQYSHPSRTHLKVKTSDRDLNRAENGLSRAHSSSEETSSVLQPGIAMETRGLADS
GQGSFTGQGIARLSRLIFLLRRWAARHVHHQDQGPDSFPDRFRGAELKEVSSQESNAQAN
VGSQEPADRGRSAWPLAKCNTNTSNNTEEEKKTKKKDAIVVDPSSNLYYRWLTAIALPVF
YNWYLLICRACFDELQSEYLMLWLVLDYSADVLYVLDVLVRARTGFLEQGLMVSDTNRLW
QHYKTTTQFKLDVLSLVPTDLAYLKVGTNYPEVRFNRLLKFSRLFEFFDRTETRTNYPNM
FRIGNLVLYILIIIHWNACIYFAISKFIGFGTDSWVYPNISIPEHGRLSRKYIYSLYWST
LTLTTIGETPPPVKDEEYLFVVVDFLVGVLIFATIVGNVGSMISNMNASRAEFQAKIDSI
KQYMQFRKVTKDLETRVIRWFDYLWANKKTVDEKEVLKSLPDKLKAEIAINVHLDTLKKV
RIFQDCEAGLLVELVLKLRPTVFSPGDYICKKGDIGKEMYIINEGKLAVVADDGVTQFVV
LSDGSYFGEISILNIKGSKSGNRRTANIRSIGYSDLFCLSKDDLMEALTEYPEAKKALEE
KGRQILMKDNLIDEELARAGADPKDLEEKVEQLGSSLDTLQTRFARLLAEYNATQMKMKQ
RLSQLESQVKGGGDKPLADGEVPGDATKTEDKQQ

Sequence length

694

Interactions

View interactions

	KEGG
	cAMP signaling pathway Olfactory transduction

Show/Hide Causal Diseases (6)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Achromatopsia	achromatopsia 2, achromatopsia, achromatopsia 3	rs104893613, rs138958917, rs104893617, rs1574390811, rs1558820134, rs1464167194, rs552069173, rs1692509021, rs761554853, rs201747279, rs374258471, rs104893621, rs104893614, rs777509481, rs137852608 View all (33 more)	N/A
Cone Dystrophy	cone dystrophy	rs117522010, rs1692799480	N/A
cone-rod dystrophy	Cone-rod dystrophy	rs1464167194	N/A
retinal dystrophy	Retinal dystrophy	rs552069173, rs761554853, rs201747279, rs104893620, rs104893613, rs138958917, rs104893617, rs749842881, rs762668060, rs183838250, rs374258471, rs137852608, rs943314733, rs104893621, rs104893614 View all (16 more)	N/A
Macular dystrophy	macular dystrophy	rs141386891	N/A
Optic Atrophy	optic atrophy	rs104893620	N/A

Show/Hide Text Mining Associations (21)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenocarcinoma	Associate	28350845
Aphasia Conduction	Associate	35704304
Atrophy	Associate	35456423
Carcinogenesis	Associate	28350845
Color Vision Defects	Associate	12205108, 14715947, 18636117, 20454696, 22901948, 24504161, 24676353, 25052312, 25277229, 26493561, 29618791, 31237654, 32352493, 32832242, 32913385 View all (14 more)
Cone Dystrophy	Associate	12205108, 25052312, 35456423
Cone Rod Dystrophies	Associate	25052312
Dyskinesias	Associate	32352493
Glioblastoma	Associate	37100462
Hypertensive Retinopathy	Associate	35233102
Leber Congenital Amaurosis	Associate	21901789, 25052312
Myopia	Associate	35456423
Nystagmus Pathologic	Associate	34703197
Photophobia	Associate	32352493
Refsum Disease Infantile	Associate	35456422, 37778667
Retinal Cone Dystrophy 1	Associate	35233102
Retinal Degeneration	Associate	35456422
Retinal Diseases	Associate	21901789, 31877759, 32423767
Space Motion Sickness	Associate	37778667
Uniparental Disomy	Associate	34360608
Vision Disorders	Associate	32352493

CNGA3 (cyclic nucleotide gated channel subunit alpha 3)