CLCA4

chloride channel accessory 4, the group of Chloride channel accessory

Basic information

Region (hg38): 1:86547078-86580754

Links

ENSG00000016602 ∙ NCBI:22802 ∙ OMIM:616857 ∙ HGNC:2018 ∙ Uniprot:Q14CN2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cystic fibrosis (Supportive), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLCA4 gene.

• not_specified (116 variants)
• not_provided (9 variants)
• Autism (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLCA4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012128.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	1	4
missense			108	10	1	119
nonsense			1			1
start loss						0
frameshift				1		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	109	14	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLCA4	protein_coding	protein_coding	ENST00000370563	14	33677

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.96e-15	0.364	124941	0	367	125308	0.00147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.231	468	482	0.970	0.0000235	6072
Missense in Polyphen		120	142.49	0.84215		1890
Synonymous	0.121	168	170	0.988	0.00000874	1765
Loss of Function	1.41	27	36.1	0.747	0.00000175	453

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00741	0.00727
Ashkenazi Jewish	0.000102	0.0000993
East Asian	0.000283	0.000272
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00169	0.00167
Middle Eastern	0.000283	0.000272
South Asian	0.00129	0.00127
Other	0.00121	0.00115

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in mediating calcium-activated chloride conductance.
• Pathway: Renin secretion - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Stimuli-sensing channels;Ion channel transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.946
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.71

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.112
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clca4b
• Phenotype: normal phenotype

Gene ontology

• Biological process: proteolysis;ion transmembrane transport;chloride transmembrane transport
• Cellular component: extracellular region;plasma membrane;integral component of plasma membrane;apical plasma membrane
• Molecular function: metalloendopeptidase activity;intracellular calcium activated chloride channel activity;chloride channel activity;metal ion binding