CNGA2

cyclic nucleotide gated channel subunit alpha 2, the group of Cyclic nucleotide gated channels

Basic information

Region (hg38): X:151734746-151745564

Previous symbols: [ "CNCA1", "CNCA" ]

Links

ENSG00000183862 ∙ NCBI:1260 ∙ OMIM:300338 ∙ HGNC:2149 ∙ Uniprot:Q16280 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• isolated congenital anosmia (Supportive), mode of inheritance: AD
• anosmia (Limited), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CNGA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNGA2 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				5	3	8
missense			46	3	6	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	46	8	9

Variants in CNGA2

This is a list of pathogenic ClinVar variants found in the CNGA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-151738497-C-A		not specified	Uncertain significance (Jun 10, 2024)
X-151738527-A-C			Benign (Apr 23, 2018)
X-151738556-A-G		not specified	Uncertain significance (May 02, 2024)
X-151738589-A-G		not specified	Conflicting classifications of pathogenicity (Sep 13, 2023)
X-151738784-C-T			Benign (Dec 31, 2019)
X-151738800-G-C		not specified	Uncertain significance (Mar 31, 2024)
X-151738805-C-T			Likely benign (Mar 01, 2023)
X-151739588-G-C		not specified	Uncertain significance (Jan 16, 2024)
X-151739612-G-A		not specified	Uncertain significance (Apr 09, 2024)
X-151739641-C-G		not specified	Uncertain significance (Dec 05, 2022)
X-151739660-C-T		not specified	Uncertain significance (Aug 28, 2024)
X-151739681-C-A		not specified	Uncertain significance (Feb 10, 2022)
X-151739689-G-C		not specified	Uncertain significance (Apr 18, 2023)
X-151739696-G-T			Benign (Dec 31, 2019)
X-151739710-G-C			Benign (Dec 31, 2019)
X-151739716-G-A		not specified	Likely benign (Dec 20, 2022)
X-151739729-C-T		not specified	Uncertain significance (Jun 11, 2024)
X-151740821-C-T			Benign (Dec 31, 2019)
X-151740867-C-A		not specified	Uncertain significance (Aug 08, 2023)
X-151742616-C-T			Likely benign (Dec 31, 2019)
X-151742636-C-T		not specified	Uncertain significance (May 26, 2024)
X-151742637-G-A		not specified	Conflicting classifications of pathogenicity (Oct 07, 2024)
X-151743137-C-T			Uncertain significance (Sep 21, 2015)
X-151743138-G-A			Benign (Jul 10, 2018)
X-151743206-T-C		not specified	Uncertain significance (Feb 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNGA2	protein_coding	protein_coding	ENST00000329903	6	6854

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000982	0.988	125720	8	12	125740	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0285	273	272	1.00	0.0000219	4365
Missense in Polyphen		111	118.43	0.9373		1953
Synonymous	-0.294	109	105	1.04	0.00000806	1308
Loss of Function	2.24	8	18.3	0.436	0.00000158	277

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000731	0.0000731
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000722	0.0000544
Finnish	0.0000626	0.0000462
European (Non-Finnish)	0.000172	0.000123
Middle Eastern	0.0000722	0.0000544
South Asian	0.000105	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Odorant signal transduction is probably mediated by a G- protein coupled cascade using cAMP as second messenger. The olfactory channel can be shown to be activated by cyclic nucleotides which leads to a depolarization of olfactory sensory neurons.
• 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: 0.114

Intolerance Scores

• loftool: 0.0646
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.61

Haploinsufficiency Scores

• pHI: 0.290
• hipred: Y
• hipred_score: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.132

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cnga2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); craniofacial phenotype; growth/size/body region 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;calmodulin binding;cAMP binding;cGMP binding