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.	54714
Gene name Gene Name - the full gene name approved by the HGNC.	Cyclic nucleotide gated channel subunit beta 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	CNGB3
Synonyms (NCBI Gene) Gene synonyms aliases	ACHM1
Chromosome Chromosome number	8
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	8q21.3
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes the beta subunit of a cyclic nucleotide-gated ion channel. The encoded beta subunit appears to play a role in modulation of channel function in cone photoreceptors. This heterotetrameric channel is necessary for sensory transduction, and

Show/Hide all(123)

SNP ID	Visualize variation	Clinical significance	Consequence
rs6471482	A>C,G,T	Pathogenic, benign	Missense variant, stop gained, synonymous variant, coding sequence variant
rs35010099	A>G,T	Benign, likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs35365413	A>C,T	Benign, uncertain-significance, likely-benign, pathogenic	Coding sequence variant, missense variant
rs77277189	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, missense variant
rs115246141	A>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs121918344	G>A	Pathogenic	Missense variant, coding sequence variant
rs139207764	G>A	Likely-pathogenic, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs139337746	T>A,C	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs140286824	T>A,C	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs147876778	C>T	Uncertain-significance, likely-benign, benign, pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs147991883	T>C,G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, synonymous variant
rs151230930	G>A,C,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs192448853	G>A,C	Likely-pathogenic, likely-benign	Stop gained, missense variant, coding sequence variant
rs200805087	G>A	Pathogenic, likely-pathogenic	Stop gained, coding sequence variant
rs201320564	G>A	Pathogenic	Stop gained, coding sequence variant
rs201794629	C>G	Pathogenic, likely-pathogenic	Splice acceptor variant
rs267602029	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs267606739	G>A,C,T	Likely-pathogenic	Stop gained, missense variant, synonymous variant, coding sequence variant
rs368787128	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs371318766	G>C	Pathogenic	Stop gained, coding sequence variant
rs372006750	C>A,T	Pathogenic, likely-pathogenic	Splice donor variant
rs372302139	C>A,T	Pathogenic	Stop gained, missense variant, coding sequence variant
rs373270306	A>C,T	Likely-pathogenic	Missense variant, coding sequence variant
rs373862340	C>A	Pathogenic, likely-pathogenic	Stop gained, coding sequence variant
rs376711003	G>A,T	Likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant, genic upstream transcript variant, stop gained
rs397515360	G>-	Uncertain-significance, pathogenic	Coding sequence variant, frameshift variant
rs564759960	T>C	Pathogenic	Missense variant, coding sequence variant
rs745557293	A>-	Likely-pathogenic	Stop gained, coding sequence variant
rs746549330	TGTTTATCTTCATTTTCTTTT>-,TGTTTATCTTCATTTTCTTTTTGTTTATCTTCATTTTCTTTT	Likely-pathogenic, conflicting-interpretations-of-pathogenicity	Inframe insertion, inframe deletion, coding sequence variant
rs748993388	->A	Likely-pathogenic	Coding sequence variant, frameshift variant
rs750257554	C>T	Likely-pathogenic	Splice acceptor variant
rs764742792	G>A,T	Likely-pathogenic	Synonymous variant, coding sequence variant, stop gained
rs768345097	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs768735888	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs770786127	G>A	Pathogenic	Stop gained, coding sequence variant
rs772725807	T>C	Pathogenic	Splice acceptor variant
rs773372519	A>C,G	Pathogenic, likely-pathogenic	Intron variant
rs773381712	A>-	Pathogenic	Frameshift variant, coding sequence variant
rs775038513	A>C,G	Pathogenic	Stop gained, synonymous variant, coding sequence variant
rs775796581	AGTCTGGG>-	Pathogenic	Frameshift variant, coding sequence variant
rs776896038	A>-,AA	Pathogenic, likely-pathogenic	Frameshift variant, coding sequence variant
rs786204492	G>A	Likely-pathogenic	5 prime UTR variant, stop gained, coding sequence variant
rs786204498	G>A	Pathogenic, likely-pathogenic	Stop gained, coding sequence variant, genic upstream transcript variant
rs786204762	C>T	Pathogenic, likely-pathogenic	Stop gained, coding sequence variant
rs886063161	TTTGTAGAAGT>A,T	Pathogenic, likely-pathogenic	Frameshift variant, coding sequence variant
rs964530890	A>C	Likely-pathogenic	Intron variant
rs998703203	G>A,T	Pathogenic, likely-pathogenic	Intron variant
rs999921351	C>T	Pathogenic	Coding sequence variant, stop gained
rs1000861056	C>T	Pathogenic	Intron variant
rs1052078370	G>A,C	Pathogenic	Missense variant, genic upstream transcript variant, coding sequence variant, stop gained
rs1057516504	C>T	Likely-pathogenic	Splice acceptor variant
rs1057516571	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1057516782	->T	Likely-pathogenic	Frameshift variant, genic upstream transcript variant, coding sequence variant
rs1057516791	T>-	Likely-pathogenic	Frameshift variant, coding sequence variant, 5 prime UTR variant
rs1057516825	C>T	Likely-pathogenic	Splice donor variant
rs1057516866	A>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1057516878	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1057517052	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1057517053	CCTG>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1057517167	T>A	Likely-pathogenic	Splice acceptor variant
rs1057517388	T>C	Likely-pathogenic	Splice acceptor variant
rs1057517434	AG>-	Likely-pathogenic	Frameshift variant, genic upstream transcript variant, coding sequence variant
rs1057517454	A>G	Likely-pathogenic	Splice donor variant
rs1057518098	->TAAT	Likely-pathogenic	Coding sequence variant, stop gained
rs1064796793	C>T	Likely-pathogenic	Splice donor variant
rs1174949911	C>G,T	Likely-pathogenic	Missense variant, coding sequence variant
rs1189928623	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1201521544	C>A,G	Likely-pathogenic, pathogenic	Splice donor variant
rs1233466909	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1358283016	C>-	Pathogenic	Genic upstream transcript variant, coding sequence variant, frameshift variant
rs1362472371	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs1375507464	C>A,G,T	Pathogenic	Splice donor variant
rs1385347376	T>C	Pathogenic	Splice acceptor variant
rs1391492794	A>G	Pathogenic	Splice donor variant
rs1442286151	->T	Pathogenic	Coding sequence variant, frameshift variant, genic upstream transcript variant
rs1554604525	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs1554604552	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs1554604767	C>T	Pathogenic, likely-pathogenic	Splice donor variant
rs1554604775	C>A	Likely-pathogenic	Coding sequence variant, stop gained
rs1554604833	A>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1554604851	T>G	Pathogenic	Splice acceptor variant
rs1554607546	C>-	Likely-pathogenic	Coding sequence variant, splice donor variant
rs1554607548	->C	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1554607553	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1554608319	A>T	Pathogenic	Coding sequence variant, stop gained
rs1554609943	G>C	Likely-pathogenic	Splice donor variant
rs1554609946	->GTCG	Pathogenic	Coding sequence variant, frameshift variant
rs1554609956	T>AC	Pathogenic	Coding sequence variant, frameshift variant
rs1554609978	T>G	Likely-pathogenic	Splice acceptor variant
rs1554610279	CT>G	Pathogenic	Coding sequence variant, frameshift variant
rs1554610284	G>A	Pathogenic	Coding sequence variant, stop gained
rs1554610655	CA>-	Pathogenic	Coding sequence variant, frameshift variant
rs1554610668	G>A	Pathogenic	Coding sequence variant, stop gained
rs1554611860	->A	Pathogenic	Coding sequence variant, stop gained
rs1554612145	G>A	Pathogenic	Coding sequence variant, missense variant
rs1554612159	T>A	Pathogenic	Splice acceptor variant
rs1554612805	G>C	Pathogenic	Coding sequence variant, stop gained
rs1554612806	C>GTTTG	Pathogenic	Coding sequence variant, frameshift variant
rs1554613998	GTAG>-	Pathogenic	Coding sequence variant, frameshift variant
rs1554614022	T>AA	Pathogenic	Coding sequence variant, frameshift variant
rs1554614024	TAAAA>AAAAAC	Pathogenic	Coding sequence variant, frameshift variant
rs1554614038	->C	Pathogenic	Coding sequence variant, frameshift variant
rs1554614131	AA>-	Pathogenic	Coding sequence variant, frameshift variant
rs1554614157	T>A	Pathogenic	Splice acceptor variant
rs1554614402	CTT>A	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1554614423	GC>TCACCAGGA	Pathogenic	Coding sequence variant, frameshift variant, 5 prime UTR variant
rs1554618404	G>A	Pathogenic	Coding sequence variant, genic upstream transcript variant, stop gained
rs1554618413	GGTT>-	Pathogenic	Coding sequence variant, genic upstream transcript variant, frameshift variant
rs1554618417	G>A	Pathogenic	Coding sequence variant, genic upstream transcript variant, stop gained
rs1554618420	G>-	Pathogenic	Coding sequence variant, genic upstream transcript variant, frameshift variant
rs1554619292	C>-	Pathogenic	Coding sequence variant, genic upstream transcript variant, frameshift variant
rs1554619303	C>A	Pathogenic	Genic upstream transcript variant, splice acceptor variant
rs1554619498	A>G	Pathogenic	Genic upstream transcript variant, splice donor variant
rs1554619500	->T	Pathogenic	Coding sequence variant, genic upstream transcript variant, frameshift variant
rs1554619509	->C	Pathogenic	Coding sequence variant, genic upstream transcript variant, frameshift variant
rs1554619513	C>T	Pathogenic	Missense variant, initiator codon variant, genic upstream transcript variant
rs1554619514	A>G	Pathogenic	Missense variant, initiator codon variant, genic upstream transcript variant
rs1585941011	G>-	Pathogenic, uncertain-significance	Coding sequence variant, frameshift variant
rs1585942791	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1585981462	TT>-	Pathogenic	Coding sequence variant, frameshift variant
rs1585981514	TTAA>-	Pathogenic	Coding sequence variant, frameshift variant
rs1586003680	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1586047969	CTGAGACTGA>-	Pathogenic	Coding sequence variant, genic upstream transcript variant, frameshift variant

Show/Hide all(49)

miRTarBase ID	miRNA	Experiments	Reference
MIRT735113	hsa-miR-17-5p	qRT-PCR	31776299
MIRT899561	hsa-miR-1178	CLIP-seq
MIRT899562	hsa-miR-1270	CLIP-seq
MIRT899563	hsa-miR-1279	CLIP-seq
MIRT899564	hsa-miR-137	CLIP-seq
MIRT899565	hsa-miR-3153	CLIP-seq
MIRT899566	hsa-miR-3161	CLIP-seq
MIRT899567	hsa-miR-3713	CLIP-seq
MIRT899568	hsa-miR-3978	CLIP-seq
MIRT899569	hsa-miR-4293	CLIP-seq
MIRT899570	hsa-miR-4422	CLIP-seq
MIRT899571	hsa-miR-4457	CLIP-seq
MIRT899572	hsa-miR-4531	CLIP-seq
MIRT899573	hsa-miR-513b	CLIP-seq
MIRT899574	hsa-miR-595	CLIP-seq
MIRT899575	hsa-miR-596	CLIP-seq
MIRT899576	hsa-miR-597	CLIP-seq
MIRT899577	hsa-miR-620	CLIP-seq
MIRT899578	hsa-miR-668	CLIP-seq
MIRT899579	hsa-miR-890	CLIP-seq
MIRT899580	hsa-miR-9	CLIP-seq
MIRT1966864	hsa-miR-3074-3p	CLIP-seq
MIRT1966865	hsa-miR-3127-5p	CLIP-seq
MIRT1966866	hsa-miR-3199	CLIP-seq
MIRT1966867	hsa-miR-3647-3p	CLIP-seq
MIRT1966868	hsa-miR-4509	CLIP-seq
MIRT1966869	hsa-miR-4652-5p	CLIP-seq
MIRT1966870	hsa-miR-4661-5p	CLIP-seq
MIRT1966871	hsa-miR-4744	CLIP-seq
MIRT1966872	hsa-miR-4793-5p	CLIP-seq
MIRT1966873	hsa-miR-579	CLIP-seq
MIRT2202605	hsa-miR-3176	CLIP-seq
MIRT2202606	hsa-miR-34b	CLIP-seq
MIRT1966867	hsa-miR-3647-3p	CLIP-seq
MIRT2202607	hsa-miR-3674	CLIP-seq
MIRT2202608	hsa-miR-3922-3p	CLIP-seq
MIRT2202609	hsa-miR-4705	CLIP-seq
MIRT1966872	hsa-miR-4793-5p	CLIP-seq
MIRT1966873	hsa-miR-579	CLIP-seq
MIRT1966867	hsa-miR-3647-3p	CLIP-seq
MIRT1966872	hsa-miR-4793-5p	CLIP-seq
MIRT1966873	hsa-miR-579	CLIP-seq
MIRT2447298	hsa-miR-1224-5p	CLIP-seq
MIRT2447299	hsa-miR-2355-3p	CLIP-seq
MIRT2447300	hsa-miR-3915	CLIP-seq
MIRT2447301	hsa-miR-4646-3p	CLIP-seq
MIRT2447302	hsa-miR-4689	CLIP-seq
MIRT2447303	hsa-miR-4751	CLIP-seq
MIRT2447304	hsa-miR-676	CLIP-seq

Show/Hide all(28)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0001750	Component	Photoreceptor outer segment	IBA
GO:0001750	Component	Photoreceptor outer segment	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:0005222	Function	Intracellularly cAMP-activated cation channel activity	IEA
GO:0005223	Function	Intracellularly cGMP-activated cation channel activity	IBA
GO:0005223	Function	Intracellularly cGMP-activated cation channel activity	IDA	12815043, 24164424
GO:0005223	Function	Intracellularly cGMP-activated cation channel activity	IEA
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	IDA	24164424
GO:0007165	Process	Signal transduction	NAS	10888875
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	TAS	10888875
GO:0016020	Component	Membrane	IEA
GO:0017071	Component	Intracellular cyclic nucleotide activated cation channel complex	IBA
GO:0030553	Function	CGMP binding	IBA
GO:0030553	Function	CGMP binding	IDA	24164424, 37463923
GO:0030553	Function	CGMP binding	IEA
GO:0034220	Process	Monoatomic ion transmembrane transport	IEA
GO:0055085	Process	Transmembrane transport	IEA
GO:0098655	Process	Monoatomic cation transmembrane transport	IBA
GO:1902495	Component	Transmembrane transporter complex	IDA	24164424

MIM	HGNC	e!Ensembl
605080	2153	ENSG00000170289

Protein

UniProt ID

Q9NQW8

Protein name

Cyclic nucleotide-gated channel beta-3 (CNG channel beta-3) (Cone photoreceptor cGMP-gated channel subunit beta) (Cyclic nucleotide-gated cation channel beta-3) (Cyclic nucleotide-gated cation channel modulatory subunit)

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

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

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00027	cNMP_binding	542 → 631	Cyclic nucleotide-binding domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed specifically in the retina. {ECO:0000269|PubMed:10958649}.

Sequence

MFKSLTKVNKVKPIGENNENEQSSRRNEEGSHPSNQSQQTTAQEENKGEEKSLKTKSTPV
TSEEPHTNIQDKLSKKNSSGDLTTNPDPQNAAEPTGTVPEQKEMDPGKEGPNSPQNKPPA
APVINEYADAQLHNLVKRMRQRTALYKKKLVEGDLSSPEASPQTAKPTAVPPVKESDDKP
TEHYYRLLWFKVKKMPLTEYLKRIKLPNSIDSYTDRLYLLWLLLVTLAYNWNCCFIPLRL
VFPYQTADNIHYWLIADIICDIIYLYDMLFIQPRLQFVRGGDIIVDSNELRKHYRTSTKF
QLDVASIIPFDICYLFFGFNPMFRANRMLKYTSFFEFNHHLESIMDKAYIYRVIRTTGYL
LFILHINACVYYWASNYEGIGTTRWVYDGEGNEYLRCYYWAVRTLITIGGLPEPQTLFEI
VFQLLNFFSGVFVFSSLIGQMRDVIGAATANQNYFRACMDDTIAYMNNYSIPKLVQKRVR
TWYEYTWDSQRMLDESDLLKTLPTTVQLALAIDVNFSIISKVDLFKGCDTQMIYDMLLRL
KSVLYLPGDFVCKKGEIGKEMYIIKHGEVQVLGGPDGTKVLVTLKAGSVFGEISLLAAGG
GNRRTANVVAHGFANLLTLDKKTLQEILVHYPDSERILMKKARVLLKQKAKTAEATPPRK
DLALLFPPKEETPKLFKTLLGGTGKASLARLLKLKREQAAQKKENSEGGEEEGKENEDKQ
KENEDKQKENEDKGKENEDKDKGREPEEKPLDRPECTASPIAVEEEPHSVRRTVLPRGTS
RQSLIISMAPSAEGGEEVLTIEVKEKAKQ

Sequence length

809

Interactions

View interactions

	KEGG
	cAMP signaling pathway

Show/Hide Causal Diseases (7)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Achromatopsia	achromatopsia 3, achromatopsia	rs6471482, rs1554608319, rs1057517454, rs1585942791, rs267606739, rs1052078370, rs201320564, rs1057516791, rs201794629, rs1554609943, rs372302139, rs1554612145, rs1554614038, rs772725807, rs1057516571 View all (92 more)	N/A
retinal dystrophy	Retinal dystrophy	rs372006750, rs761969118, rs267606739, rs772725807, rs786204762, rs201320564, rs1554612159, rs1822989898, rs397515360, rs373862340, rs1375507464, rs775796581, rs886063161, rs1000861056, rs764742792, rs773372519, rs776896038 View all (2 more)	N/A
Retinitis Pigmentosa	retinitis pigmentosa	rs397515360	N/A
cone-rod dystrophy	Cone-rod dystrophy	rs397515360	N/A
Leber Congenital Amaurosis	leber congenital amaurosis	rs397515360, rs775796581, rs773372519	N/A
Macular dystrophy	macular dystrophy	rs1554604767	N/A
Optic Atrophy	optic atrophy	rs397515360	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Metabolic Syndrome	Metabolic syndrome	N/A	N/A	GWAS

Show/Hide Text Mining Associations (21)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Aphasia Conduction	Associate	35704304
Channelopathies	Associate	26473621
Choroideremia	Associate	23940504
Color Vision Defects	Associate	12205108, 14715947, 18636117, 20454696, 22901948, 23940504, 24504161, 24676353, 25277229, 25558176, 27479814, 28145975, 29618791, 30826882, 31237654 View all (14 more)
Color Vision Defects	Stimulate	37172884
Cone Dystrophy	Associate	28746191
Cone Rod Dystrophies	Associate	23776498, 23940504
Enhanced S Cone Syndrome	Associate	32881472
Leber Congenital Amaurosis	Associate	23940504
Myopia	Associate	31776299
Night blindness congenital stationary	Associate	32881472
Nystagmus Pathologic	Associate	34703197
Refsum Disease Infantile	Associate	35456422, 37778667, 39189993
Retinal Cone Dystrophy 1	Associate	34703197, 35233102
Retinal Degeneration	Associate	35456422
Retinal Diseases	Associate	31877759, 32423767, 38160664
Retinal Dystrophies	Associate	25943428, 27874104, 32881472
Retinitis Pigmentosa	Associate	23940504
Space Motion Sickness	Associate	37778667
Usher Syndromes	Associate	23940504
Vision Disorders	Associate	28746191, 36980963

CNGB3 (cyclic nucleotide gated channel subunit beta 3)