CNGA4

cyclic nucleotide gated channel subunit alpha 4, the group of Cyclic nucleotide gated channels

Basic information

Region (hg38): 11:6234765-6244479

Previous symbols: [ "CNCA2", "CNGB2" ]

Links

ENSG00000132259 ∙ NCBI:1262 ∙ OMIM:609472 ∙ HGNC:2152 ∙ Uniprot:Q8IV77 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CNGA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNGA4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			41	1	2	44
nonsense						0
start loss				1		1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	41	2	3

Variants in CNGA4

This is a list of pathogenic ClinVar variants found in the CNGA4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-6239207-A-G			Likely benign (Mar 29, 2018)
11-6239225-G-T		not specified	Uncertain significance (Jun 29, 2023)
11-6239234-A-T		not specified	Uncertain significance (Apr 27, 2023)
11-6239255-C-T		not specified	Uncertain significance (Feb 26, 2024)
11-6239403-G-T		not specified	Uncertain significance (Mar 29, 2023)
11-6239473-T-A		not specified	Uncertain significance (Aug 22, 2023)
11-6239478-G-A		not specified	Uncertain significance (Dec 21, 2022)
11-6239746-G-A		not specified	Uncertain significance (Mar 20, 2024)
11-6239775-G-T		not specified	Uncertain significance (Oct 09, 2024)
11-6239785-A-G		not specified	Uncertain significance (Apr 07, 2022)
11-6240139-C-A		not specified	Uncertain significance (Sep 09, 2024)
11-6240150-T-C		not specified	Uncertain significance (Sep 25, 2023)
11-6240152-G-C		not specified	Uncertain significance (Jul 19, 2023)
11-6240174-T-C		not specified	Uncertain significance (Nov 21, 2023)
11-6240185-C-T		not specified	Uncertain significance (Sep 27, 2024)
11-6240221-C-T		not specified	Uncertain significance (Sep 13, 2023)
11-6240260-C-T		not specified	Uncertain significance (Dec 14, 2021)
11-6240263-A-G			Benign (Jul 21, 2018)
11-6240296-C-T		not specified	Uncertain significance (Jun 18, 2024)
11-6240358-T-G		not specified	Uncertain significance (Dec 04, 2024)
11-6240413-G-A		not specified	Uncertain significance (Feb 21, 2024)
11-6240432-G-A		not specified	Uncertain significance (Feb 22, 2023)
11-6240480-T-C		not specified	Uncertain significance (Sep 02, 2024)
11-6240504-C-T		not specified	Likely benign (Jul 25, 2023)
11-6240535-G-C		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNGA4	protein_coding	protein_coding	ENST00000379936	6	9665

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.42e-7	0.908	125494	1	253	125748	0.00101

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0116	348	349	0.998	0.0000235	3728
Missense in Polyphen		116	128.26	0.90442		1405
Synonymous	1.03	129	145	0.891	0.00000958	1192
Loss of Function	1.71	14	22.8	0.614	0.00000126	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.00101
Ashkenazi Jewish	0.00	0.00
East Asian	0.00109	0.00109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000988	0.000976
Middle Eastern	0.00109	0.00109
South Asian	0.00284	0.00281
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Second messenger, cAMP, causes the opening of cation- selective cyclic nucleotide-gated (CNG) channels and depolarization of the neuron (olfactory sensory neurons, OSNs). CNGA4 is the modulatory subunit of this channel which is known to play a central role in the transduction of odorant signals and subsequent adaptation. By accelerating the calcium-mediated negative feedback in olfactory signaling it allows rapid adaptation to odor stimulation and extends its range of odor detection (By similarity). {ECO:0000250}.
• Pathway: cAMP signaling pathway - Homo sapiens (human);Olfactory transduction - Homo sapiens (human);NO-cGMP-PKG mediated Neuroprotection;VxPx cargo-targeting to cilium;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.153
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.17

Haploinsufficiency Scores

• pHI: 0.443
• hipred: N
• hipred_score: 0.229

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.224

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cnga4
• Phenotype: taste/olfaction phenotype

Gene ontology

• Biological process: sensory perception of smell;response to stimulus;cation transmembrane transport
• Cellular component: Golgi membrane;integral component of membrane;Golgi-associated vesicle membrane;ciliary membrane
• Molecular function: intracellular cAMP-activated cation channel activity;intracellular cGMP-activated cation channel activity;cAMP binding;cGMP binding