CNGA1 cyclic nucleotide gated channel subunit alpha 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CNGA1provided by HGNC
Official Full Name: cyclic nucleotide gated channel subunit alpha 1provided by HGNC
Primary source: HGNC:HGNC:2148
See related: Ensembl:ENSG00000198515 MIM:123825; AllianceGenome:HGNC:2148
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: CNCG; CNG1; RP49; CNCG1; CNG-1; RCNC1; RCNCa; RCNCalpha
Summary: The protein encoded by this gene is involved in phototransduction. Along with another protein, the encoded protein forms a cGMP-gated cation channel in the plasma membrane, allowing depolarization of rod photoreceptors. This represents the last step in the phototransduction pathway. Defects in this gene are a cause of retinitis pigmentosa autosomal recessive (ARRP) disease. Multiple transcript variants have been found for this gene. [provided by RefSeq, Oct 2019]
Expression: Broad expression in liver (RPKM 2.5), small intestine (RPKM 1.6) and 17 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4p12

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (47935977..48016681, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (47903221..47983754, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (47937994..48018698, complement)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

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.
A case of retinitis pigmentosa homozygous for a rare CNGA1 causal variant.
Title: A case of retinitis pigmentosa homozygous for a rare CNGA1 causal variant.
Genome-wide Association Analysis Across 16,956 Patients Identifies a Novel Genetic Association Between BMP6, NIPAL1, CNGA1 and Spondylosis.
Title: Genome-wide Association Analysis Across 16,956 Patients Identifies a Novel Genetic Association Between BMP6, NIPAL1, CNGA1 and Spondylosis.
Identification of a novel homozygous variant in the CNGA1 gene in a Chinese family with autosomal recessive retinitis pigmentosa.
Title: Identification of a novel homozygous variant in the CNGA1 gene in a Chinese family with autosomal recessive retinitis pigmentosa.
Compound heterozygous mutations (NM000087, p.Y82X and p.L89fs) in exon 6 of CNGA1are pathogenic mutations in this Chinese family affected with autosomal recessive retinitis pigmentosa. Of which, p.Y82X is firstly reported in patient with autosomal recessive retinitis pigmentosa.
Title: Novel compound heterozygous mutations in CNGA1in a Chinese family affected with autosomal recessive retinitis pigmentosa by targeted sequencing.
The mut CNGA1 p.(G513R) protein was largely retained inside the cell rather than being targeted to the plasma membrane, suggesting the absence of cGMP-gated cation channels in the plasma membrane
Title: Novel compound heterozygous mutation in the CNGA1 gene underlie autosomal recessive retinitis pigmentosa in a Chinese family.
CNGA1 mutations are one of the most frequent autosomal recessive retinitis pigmentosa-causing mutations in the Japanese patients.
Title: Whole exome analysis identifies frequent CNGA1 mutations in Japanese population with autosomal recessive retinitis pigmentosa.
Insulin receptor (IR), an integral membrane protein, directly phosphorylates the CNGA1 subunit of CNG channels that in turn affects the function of these channels negatively. CNGA1 is a direct substrate of IR.
Title: Insulin receptor regulates photoreceptor CNG channel activity.
Observational study of genetic testing. (HuGE Navigator)
Title: Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip.
isolated an endogenous transcript (anti-CNG1) that is antisense to CNG1 mRNA; data suggest the suppression of CNG(alpha)1 expression by anti-CNG1 may play an important role in neuronal functions, especially in synaptic plasticity and cortical development
Title: An endogenous RNA transcript antisense to CNG(alpha)1 cation channel mRNA.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Retinitis pigmentosa MedGen: C0035334 OMIM: 268000 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview	Compare labs
Retinitis pigmentosa 49 MedGen: C3151059 OMIM: 613756 GeneReviews: Not available	Compare labs

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

SHGC4-1079 (e-PCR)
- UniSTS:38914

PMC129976P1 (e-PCR)
- UniSTS:270606

PMC129976P2 (e-PCR)
- UniSTS:270607

G34058 (e-PCR)
- UniSTS:6697

D4S3172 (e-PCR)
- UniSTS:41286

WI-18943 (e-PCR)
- UniSTS:73598

SHGC-59576 (e-PCR)
- UniSTS:69342

D4S915 (e-PCR)
- UniSTS:30704

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 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 monoatomic cation transmembrane transport	IBA Inferred from Biological aspect of Ancestor 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	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of intracellular cyclic nucleotide activated cation channel complex	IBA Inferred from Biological aspect of Ancestor more info
located_in photoreceptor outer segment membrane	IEA Inferred from Electronic Annotation 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

General protein information

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Preferred Names: cyclic nucleotide-gated channel alpha-1

Names: CNG channel alpha-1; cGMP-gated cation channel alpha-1; cyclic nucleotide gated channel alpha 1; cyclic nucleotide-gated cation channel 1; cyclic nucleotide-gated channel, photoreceptor; interleukin-1 homologue; rod photoreceptor cGMP-gated cation channel subunit alpha; rod photoreceptor cGMP-gated channel subunit alpha

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_009193.1 RefSeqGene

Range

1264..81968

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000087.5 → NP_000078.3 cyclic nucleotide-gated channel alpha-1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2 and 3 both encode the same isoform (2).

Source sequence(s)

AC096749, AC107068

Consensus CDS

CCDS43226.2

UniProtKB/Swiss-Prot

A8K7K6, J3KPZ2, P29973, Q16279, Q16485, Q4W5E3

Related

ENSP00000389881.3, ENST00000420489.7

Conserved Domains (3) summary

cd00038
Location:475 → 591

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:161 → 403

Ion_trans; Ion transport protein

pfam16526
Location:591 → 660

CLZ; C-terminal leucine zipper domain of cyclic nucleotide-gated channels
NM_001142564.2 → NP_001136036.2 cyclic nucleotide-gated channel alpha-1

Status: REVIEWED

Description

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

Source sequence(s)

AC096749, AC107068

Consensus CDS

CCDS43226.2

UniProtKB/Swiss-Prot

A8K7K6, J3KPZ2, P29973, Q16279, Q16485, Q4W5E3

Related

ENSP00000384264.5, ENST00000402813.9

Conserved Domains (3) summary

cd00038
Location:475 → 591

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:161 → 403

Ion_trans; Ion transport protein

pfam16526
Location:591 → 660

CLZ; C-terminal leucine zipper domain of cyclic nucleotide-gated channels
NM_001379270.1 → NP_001366199.1 cyclic nucleotide-gated channel alpha-1

Status: REVIEWED

Source sequence(s)

AC096749, AC107068

Consensus CDS

CCDS43226.2

UniProtKB/Swiss-Prot

A8K7K6, J3KPZ2, P29973, Q16279, Q16485, Q4W5E3

Related

ENSP00000426862.3, ENST00000514170.7

Conserved Domains (3) summary

cd00038
Location:475 → 591

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:161 → 403

Ion_trans; Ion transport protein

pfam16526
Location:591 → 660

CLZ; C-terminal leucine zipper domain of cyclic nucleotide-gated channels

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

47935977..48016681 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005248049.5 → XP_005248106.3 cyclic nucleotide-gated channel alpha-1 isoform X1
XM_011513623.3 → XP_011511925.1 cyclic nucleotide-gated channel alpha-1 isoform X1

See identical proteins and their annotated locations for XP_011511925.1

Conserved Domains (3) summary

cd00038
Location:479 → 595

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:165 → 407

Ion_trans; Ion transport protein

pfam16526
Location:595 → 664

CLZ; C-terminal leucine zipper domain of cyclic nucleotide-gated channels

Alternate T2T-CHM13v2.0

Genomic

NC_060928.1 Alternate T2T-CHM13v2.0

Range

47903221..47983754 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054348882.1 → XP_054204857.1 cyclic nucleotide-gated channel alpha-1 isoform X1
XM_054348881.1 → XP_054204856.1 cyclic nucleotide-gated channel alpha-1 isoform X1