CNGB1 cyclic nucleotide gated channel subunit beta 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CNGB1provided by HGNC
Official Full Name: cyclic nucleotide gated channel subunit beta 1provided by HGNC
Primary source: HGNC:HGNC:2151
See related: Ensembl:ENSG00000070729 MIM:600724; AllianceGenome:HGNC:2151
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CNG4; GAR1; GARP; RP45; CNCG2; CNCG4; GARP2; RCNC2; RCNCb; CNCG3L; CNGB1B; RCNCbeta
Summary: In humans, the rod photoreceptor cGMP-gated cation channel helps regulate ion flow into the rod photoreceptor outer segment in response to light-induced alteration of the levels of intracellular cGMP. This channel consists of two subunits, alpha and beta, with the protein encoded by this gene representing the beta subunit. Defects in this gene are a cause of cause of retinitis pigmentosa type 45. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2013]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 16q21

Exon count:: 34

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (57882340..57971128, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (63677581..63766382, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (57916244..58005032, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Development of a translatable gene augmentation therapy for CNGB1-retinitis pigmentosa.
Title: Development of a translatable gene augmentation therapy for CNGB1-retinitis pigmentosa.
Structural basis of the partially open central gate in the human CNGA1/CNGB1 channel explained by additional density for calmodulin in cryo-EM map.
Title: Structural basis of the partially open central gate in the human CNGA1/CNGB1 channel explained by additional density for calmodulin in cryo-EM map.
CNGB1-related rod-cone dystrophy: A mutation review and update.
Title: CNGB1-related rod-cone dystrophy: A mutation review and update.
Functional Evaluation of Splicing for Variants of Uncertain Significance in Patients with Inherited Retinal Diseases.
Title: Functional Evaluation of Splicing for Variants of Uncertain Significance in Patients with Inherited Retinal Diseases.
Variable expressivity in patients with autosomal recessive retinitis pigmentosa associated with the gene CNGB1.
Title: Variable expressivity in patients with autosomal recessive retinitis pigmentosa associated with the gene CNGB1.
Mutations in CNGB1 may cause an autosomal recessive retinitis pigmentosa-olfactory dysfunction syndrome characterized by a slow progression of retinal degeneration and variable anosmia or hyposmia.
Title: Olfactory Dysfunction in Patients With CNGB1-Associated Retinitis Pigmentosa.
The c.385delC (p.(L129WfsTer148)) mutation in the CNGB1 gene screened by exome sequencing is probably responsible for the retinitis pigmentosa phenotype in this family.
Title: Identification of a CNGB1 Frameshift Mutation in a Han Chinese Family with Retinitis Pigmentosa.
Patients and animal models of CNGbeta1-deficient retinitis pigmentosa support gene augmentation approach.
Title: Patients and animal models of CNGβ1-deficient retinitis pigmentosa support gene augmentation approach.
Here, we present the first case of RP45 caused by an unequivocal homozygous nonsense variant of CNGB1 identified by run of homozygosity (ROH) analysis.
Title: Run of homozygosity analysis reveals a novel nonsense variant of the CNGB1 gene involved in retinitis pigmentosa 45.
Helios, and not FoxP3, is the marker of activated Tregs expressing GARP/LAP, and FoxP3+Helios+ Tregs have more suppressive characteristics, compared with FoxP3+Helios- Tregs.
Title: Helios, and not FoxP3, is the marker of activated Tregs expressing GARP/LAP.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Retinitis pigmentosa 45 MedGen: C3151066 OMIM: 613767 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

L17694 (e-PCR)
- UniSTS:14594

G63062 (e-PCR)
- UniSTS:140037

MARC_10217-10218:998404657:1 (e-PCR)
- UniSTS:267070

SHGC-32528 (e-PCR)
- UniSTS:19871

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cAMP binding	IDA Inferred from Direct Assay more info	PubMed
enables cGMP binding	IBA Inferred from Biological aspect of Ancestor more info
enables cGMP binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium channel activity	IEA Inferred from Electronic Annotation more info
enables intracellularly cAMP-activated cation channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables intracellularly cAMP-activated cation channel activity	IDA Inferred from Direct Assay more info	PubMed
enables intracellularly cGMP-activated cation channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables intracellularly cGMP-activated cation channel activity	IDA Inferred from Direct Assay more info	PubMed
enables ligand-gated monoatomic ion channel activity	TAS Traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IBA Inferred from Biological aspect of Ancestor more info
enables sodium channel activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in calcium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in calcium ion transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in detection of chemical stimulus involved in sensory perception of smell	ISS Inferred from Sequence or Structural Similarity more info
involved_in detection of light stimulus involved in visual perception	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ion channel modulating, G protein-coupled receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in membrane depolarization	ISS Inferred from Sequence or Structural Similarity more info
involved_in monoatomic cation transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in monoatomic cation transport	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of olfactory nerve maturation	ISS Inferred from Sequence or Structural Similarity more info
involved_in photoreceptor cell maintenance	IEA Inferred from Electronic Annotation more info
involved_in photoreceptor cell outer segment organization	IEA Inferred from Electronic Annotation more info
involved_in phototransduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in potassium ion transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to organelle	IEA Inferred from Electronic Annotation more info
involved_in regulation of cytosolic calcium ion concentration	IEA Inferred from Electronic Annotation more info
involved_in response to odorant	ISS Inferred from Sequence or Structural Similarity more info
involved_in retina homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in retina homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within sensory perception of smell	ISS Inferred from Sequence or Structural Similarity more info
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in sodium ion transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in visual perception	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in Golgi-associated vesicle membrane	TAS Traceable Author Statement more info
located_in ciliary membrane	TAS Traceable Author Statement more info
part_of intracellular cyclic nucleotide activated cation channel complex	IBA Inferred from Biological aspect of Ancestor more info
located_in non-motile cilium membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in photoreceptor outer segment	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in rod photoreceptor outer segment	ISS Inferred from Sequence or Structural Similarity more info
located_in terminal bouton	IEA Inferred from Electronic Annotation more info
part_of transmembrane transporter complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: cyclic nucleotide-gated channel beta-1

Names: CNG channel beta-1; CNG-4; cyclic nucleotide gated channel beta 1; cyclic nucleotide-gated cation channel 4; cyclic nucleotide-gated cation channel beta-1; cyclic nucleotide-gated cation channel gamma; cyclic nucleotide-gated cation channel modulatory subunit; glutamic-acid-rich protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_016351.1 RefSeqGene

Range

4989..93777

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001135639.2 → NP_001129111.1 cyclic nucleotide-gated channel beta-1 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate exon and lacks the 3' coding region, compared to variant 1. The resulting isoform (b), also known as GARP2, is much shorter and has a unique C-terminus, compared to isoform a.

Source sequence(s)

AC010543, BM672421, BQ638084, EL945866, U18945

Consensus CDS

CCDS45495.1

UniProtKB/Swiss-Prot

Q14028

Related

ENSP00000311670.4, ENST00000311183.8

Conserved Domains (1) summary

PRK14971
Location:166 → 254

PRK14971; DNA polymerase III subunits gamma and tau; Provisional
NM_001286130.2 → NP_001273059.1 cyclic nucleotide-gated channel beta-1 isoform c

See identical proteins and their annotated locations for NP_001273059.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AC010543, AF042498, BM678849, U18945, U58837

Consensus CDS

CCDS67042.1

UniProtKB/Swiss-Prot

Q14028

Related

ENSP00000454633.1, ENST00000564448.5

Conserved Domains (4) summary

pfam05887
Location:171 → 251

Trypan_PARP; Procyclic acidic repetitive protein (PARP)

COG0664
Location:950 → 1087

Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]

cd00038
Location:956 → 1065

CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

pfam00520
Location:668 → 875

Ion_trans; Ion transport protein
NM_001297.5 → NP_001288.3 cyclic nucleotide-gated channel beta-1 isoform a

See identical proteins and their annotated locations for NP_001288.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AC010543, BM678849, U18945, U58837

Consensus CDS

CCDS42169.1

UniProtKB/Swiss-Prot

H3BN09, O43636, Q13059, Q14028, Q14029, Q9UMG2

Related

ENSP00000251102.8, ENST00000251102.13

Conserved Domains (4) summary

pfam05887
Location:171 → 257

Trypan_PARP; Procyclic acidic repetitive protein (PARP)

COG0664
Location:956 → 1093

Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]

cd00038
Location:962 → 1071

CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

pfam00520
Location:674 → 881

Ion_trans; Ion transport protein