CNGA3 cyclic nucleotide gated channel subunit alpha 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CNGA3provided by HGNC
Official Full Name: cyclic nucleotide gated channel subunit alpha 3provided by HGNC
Primary source: HGNC:HGNC:2150
See related: Ensembl:ENSG00000144191 MIM:600053; AllianceGenome:HGNC:2150
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: CNG3; ACHM2; CCNC1; CCNCa; CNCG3; CCNCalpha
Summary: 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. Two alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 2q11.2

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (98346456..98398601)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (98804385..98856818)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (98962919..99015064)

Chromosome 2 - NC_000002.12 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 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?

Functional evaluation allows ACMG/AMP-based re-classification of CNGA3 variants associated with achromatopsia.
Title: Functional evaluation allows ACMG/AMP-based re-classification of CNGA3 variants associated with achromatopsia.
Molecular and Clinical Characterization of CNGA3 and CNGB3 Genes in Brazilian Patients Affected with Achromatopsia.
Title: Molecular and Clinical Characterization of CNGA3 and CNGB3 Genes in Brazilian Patients Affected with Achromatopsia.
Systematic analysis of CNGA3 splice variants identifies different mechanisms of aberrant splicing.
Title: Systematic analysis of CNGA3 splice variants identifies different mechanisms of aberrant splicing.
Comprehensive variant spectrum of the CNGA3 gene in patients affected by achromatopsia.
Title: Comprehensive variant spectrum of the CNGA3 gene in patients affected by achromatopsia.
Delineating the Molecular and Phenotypic Spectrum of the CNGA3-Related Cone Photoreceptor Disorder in Pakistani Families.
Title: Delineating the Molecular and Phenotypic Spectrum of the CNGA3-Related Cone Photoreceptor Disorder in Pakistani Families.
Structural and functional characterization of an achromatopsia-associated mutation in a phototransduction channel.
Title: Structural and functional characterization of an achromatopsia-associated mutation in a phototransduction channel.
Disease Progression in CNGA3 and CNGB3 Retinopathy; Characteristics of Slovenian Cohort and Proposed OCT Staging Based on Pooled Data from 126 Patients from 7 Studies.
Title: Disease Progression in CNGA3 and CNGB3 Retinopathy; Characteristics of Slovenian Cohort and Proposed OCT Staging Based on Pooled Data from 126 Patients from 7 Studies.
Molecular and clinical characterization of Thai patients with achromatopsia: identification of three novel disease-associated variants in the CNGA3 and CNGB3 genes.
Title: Molecular and clinical characterization of Thai patients with achromatopsia: identification of three novel disease-associated variants in the CNGA3 and CNGB3 genes.
Mutations in CNGA3 gene c.1306 C>T (p.R436W) and a novel variant c.1540G>A (p.D514N) were described in Pakistan families with Autosomal Recessive Achromatopsia.
Title: Identification of Novel Mutation in CNGA3 gene by Whole-Exome Sequencing and In-Silico Analyses for Genotype-Phenotype Assessment with Autosomal Recessive Achromatopsia in Pakistani families.
Diseases associated with mutations in CNGA3: Genotype-phenotype correlation.
Title: Diseases associated with mutations in CNGA3: Genotype-phenotype correlation and diagnostic guideline.

Submit: New GeneRIF Correction See all GeneRIFs (53)

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
Achromatopsia 2 MedGen: C1857618 OMIM: 216900 GeneReviews: Achromatopsia	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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cGMP binding	IBA Inferred from Biological aspect of Ancestor more info
enables cGMP binding	IDA Inferred from Direct Assay more info	PubMed
enables cGMP binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables cadherin binding	IEA Inferred from Electronic Annotation more info
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 intracellularly cGMP-activated cation channel activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables ligand-gated monoatomic ion channel activity	TAS Traceable Author Statement more info	PubMed
enables myosin binding	IEA Inferred from Electronic Annotation more info
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 inorganic cation import across plasma membrane	IEA Inferred from Electronic Annotation more info
involved_in monoatomic cation transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in monoatomic cation transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to cAMP	IEA Inferred from Electronic Annotation more info
involved_in response to magnesium ion	IEA Inferred from Electronic Annotation more info
involved_in signal transduction	TAS Traceable Author Statement more info	PubMed
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in axon initial segment	IEA Inferred from Electronic Annotation more info
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in glial cell projection	IEA Inferred from Electronic Annotation more info
part_of intracellular cyclic nucleotide activated cation channel complex	IBA Inferred from Biological aspect of Ancestor more info
located_in perikaryon	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	IDA Inferred from Direct Assay more info	PubMed
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 alpha-3

Names: CNG channel alpha-3; CNG-3; cone photoreceptor cGMP-gated channel alpha subunit; cone photoreceptor cGMP-gated channel subunit alpha; cone photoreceptor cGMP-gated channel subunit alpha-3; cyclic nucleotide gated channel alpha 3; cyclic nucleotide-gated cation channel alpha-3

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_009097.1 RefSeqGene

Range

5302..57447

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001079878.2 → NP_001073347.1 cyclic nucleotide-gated channel alpha-3 isoform 2

See identical proteins and their annotated locations for NP_001073347.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region, compared to variant 1. The resulting protein (isoform 2) is shorter and lacks an internal segment, compared to isoform 1.

Source sequence(s)

AC092675, BC096299, DR002103

Consensus CDS

CCDS42719.1

UniProtKB/Swiss-Prot

Q16281

Related

ENSP00000410070.2, ENST00000436404.6

Conserved Domains (4) summary

COG0664
Location:458 → 628

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

cd00038
Location:464 → 580

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:168 → 392

Ion_trans; Ion transport protein

pfam16526
Location:580 → 650

CLZ; C-terminal leucine zipper domain of cyclic nucleotide-gated channels
NM_001298.3 → NP_001289.1 cyclic nucleotide-gated channel alpha-3 isoform 1

See identical proteins and their annotated locations for NP_001289.1

Status: REVIEWED

Description

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

Source sequence(s)

AC092675

Consensus CDS

CCDS2034.1

UniProtKB/Swiss-Prot

E9PF93, Q16281, Q4VAP7, Q53RD2, Q6ZNA7, Q9UP64

Related

ENSP00000272602.2, ENST00000272602.7

Conserved Domains (3) summary

cd00038
Location:482 → 598

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:168 → 410

Ion_trans; Ion transport protein

pfam16526
Location:598 → 668

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_000002.12 Reference GRCh38.p14 Primary Assembly

Range

98346456..98398601

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011510554.3 → XP_011508856.1 cyclic nucleotide-gated channel alpha-3 isoform X1

Conserved Domains (4) summary

COG0664
Location:531 → 701

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

cd00038
Location:537 → 653

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:241 → 465

Ion_trans; Ion transport protein

pfam16526
Location:653 → 723

CLZ; C-terminal leucine zipper domain of cyclic nucleotide-gated channels
XM_047443222.1 → XP_047299178.1 cyclic nucleotide-gated channel alpha-3 isoform X1
XM_006712243.3 → XP_006712306.1 cyclic nucleotide-gated channel alpha-3 isoform X2

Conserved Domains (4) summary

COG0664
Location:513 → 683

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

cd00038
Location:519 → 635

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:223 → 447

Ion_trans; Ion transport protein

pfam16526
Location:635 → 705

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

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

98804385..98856818

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054340429.1 → XP_054196404.1 cyclic nucleotide-gated channel alpha-3 isoform X1
XM_054340428.1 → XP_054196403.1 cyclic nucleotide-gated channel alpha-3 isoform X1
XM_054340430.1 → XP_054196405.1 cyclic nucleotide-gated channel alpha-3 isoform X2