CLXN

calaxin, the group of Outer dynein arm docking complex subunits|EF-hand domain containing

Basic information

Region (hg38): 8:48710789-48735311

Previous symbols: [ "EFCAB1" ]

Links

ENSG00000034239 ∙ NCBI:79645 ∙ OMIM:619564 ∙ HGNC:25678 ∙ Uniprot:Q9HAE3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 53	AR	Allergy/Immunology/Infectious; Cardiovascular; Pulmonary	Pulmonary surveillance may be beneficial to assess respiratory function and institute early management measures; In order to facilitate mucus clearance, interventions including vaccinations and early and aggressive treatment of respiratory infections may be beneficial; The condition can involve multiple anomalies, and individuals may require surgery or other interventions related to findings such as congenital cardiac malformations	Allergy/Immunology/Infectious; Cardiovascular; Gastrointestinal; Neurologic; Pulmonary	36727596

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLXN 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			11			11
nonsense		2				2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	2	12	0	0

Variants in CLXN

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

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

Position	Type	Phenotype	Significance	ClinVar
8-48724801-T-A		not specified	Uncertain significance (Aug 16, 2021)
8-48729040-AC-A		Ciliary dyskinesia, primary, 53	Uncertain significance (Sep 04, 2024)
8-48729117-A-T		not specified	Uncertain significance (May 11, 2022)
8-48729824-C-A		Ciliary dyskinesia, primary, 53	Likely pathogenic (Mar 03, 2024)
8-48729838-C-A		not specified	Uncertain significance (Jan 17, 2023)
8-48729844-C-A		not specified	Uncertain significance (Mar 22, 2023)
8-48730547-T-G		not specified	Uncertain significance (Feb 27, 2023)
8-48730566-C-T		not specified	Uncertain significance (Feb 22, 2025)
8-48730567-G-A		Ciliary dyskinesia, primary, 53	Likely pathogenic (Mar 03, 2024)
8-48730638-C-T		not specified	Uncertain significance (Jun 16, 2024)
8-48731365-T-C		not specified	Uncertain significance (May 20, 2024)
8-48731371-G-C		not specified	Uncertain significance (Dec 27, 2022)
8-48731379-A-C		not specified	Uncertain significance (Feb 01, 2025)
8-48731413-C-T		not specified	Uncertain significance (Mar 28, 2023)
8-48731432-GACCTTGCCTCTCT-G		Ciliary dyskinesia, primary, 53	Pathogenic (Dec 01, 2023)
8-48731446-A-G		not specified	Uncertain significance (Aug 01, 2024)
8-48731477-T-C		not specified	Uncertain significance (May 10, 2024)
8-48735123-G-C		not specified	Uncertain significance (Feb 19, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLXN	protein_coding	protein_coding	ENST00000262103	6	24523

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000277	0.802	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0699	103	105	0.981	0.00000485	1421
Missense in Polyphen		24	31.953	0.7511		453
Synonymous	0.196	35	36.5	0.959	0.00000168	362
Loss of Function	1.14	7	11.1	0.630	6.74e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000140	0.000139
European (Non-Finnish)	0.0000619	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.0000667	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0990

Intolerance Scores

• loftool: 0.643
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.350
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.310

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efcab1

Gene ontology

• Molecular function: calcium ion binding