CLCA4

chloride channel accessory 4, the group of Chloride channel accessory

Basic information

Region (hg38): 1:86547077-86580754

Links

ENSG00000016602 ∙ NCBI:22802 ∙ OMIM:616857 ∙ HGNC:2018 ∙ Uniprot:Q14CN2 ∙ 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 CLCA4 gene.

• Inborn genetic diseases (35 variants)
• not provided (6 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.

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				1	2	3
missense			33	2	1	36
nonsense			1			1
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	4	3

Variants in CLCA4

This is a list of pathogenic ClinVar variants found in the CLCA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-86547216-G-A		not specified	Uncertain significance (Dec 06, 2023)
1-86547234-G-C		not specified	Uncertain significance (Jan 17, 2023)
1-86559948-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-86560244-G-A		not specified	Uncertain significance (May 03, 2023)
1-86560249-A-G			Benign/Likely benign (Dec 01, 2023)
1-86560256-C-A		not specified	Uncertain significance (May 11, 2022)
1-86560311-C-T		not specified	Uncertain significance (Apr 12, 2022)
1-86560314-CT-C			Likely benign (Dec 31, 2019)
1-86560334-A-C		not specified	Uncertain significance (Sep 16, 2021)
1-86563694-G-A		not specified	Uncertain significance (Apr 06, 2022)
1-86565281-G-A		not specified	Likely benign (Sep 13, 2023)
1-86565809-A-T		not specified	Uncertain significance (Apr 11, 2023)
1-86565827-C-A		not specified	Likely benign (Dec 12, 2023)
1-86565886-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-86565904-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-86565949-C-T		not specified	Uncertain significance (Aug 08, 2023)
1-86565961-T-C			Benign (Mar 29, 2018)
1-86565997-C-T		not specified	Uncertain significance (Apr 01, 2022)
1-86567433-C-T		not specified	Uncertain significance (Aug 30, 2021)
1-86567452-A-G		not specified	Uncertain significance (Sep 23, 2023)
1-86567505-A-T		not specified	Uncertain significance (Nov 27, 2023)
1-86567527-C-T		not specified	Uncertain significance (May 31, 2023)
1-86567532-A-G		not specified	Uncertain significance (May 17, 2023)
1-86567572-G-A		not specified	Uncertain significance (Sep 06, 2022)
1-86567611-G-A		not specified	Uncertain significance (Feb 03, 2022)

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