CLCA1

chloride channel accessory 1, the group of Chloride channel accessory

Basic information

Region (hg38): 1:86468367-86500259

Links

ENSG00000016490 ∙ NCBI:1179 ∙ OMIM:603906 ∙ HGNC:2015 ∙ Uniprot:A8K7I4 ∙ 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 CLCA1 gene.

• Inborn genetic diseases (31 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLCA1 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			28	3	4	35
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	28	3	4

Variants in CLCA1

This is a list of pathogenic ClinVar variants found in the CLCA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-86468986-G-C		not specified	Uncertain significance (Jan 24, 2024)
1-86468986-G-T		not specified	Uncertain significance (Jul 16, 2021)
1-86469056-A-C		not specified	Uncertain significance (Jun 02, 2023)
1-86469080-G-A		not specified	Likely benign (Sep 16, 2021)
1-86473760-C-T		not specified	Uncertain significance (Sep 14, 2023)
1-86473774-C-T		not specified	Uncertain significance (Aug 05, 2023)
1-86473813-G-A		not specified	Uncertain significance (Dec 14, 2022)
1-86473857-A-T		not specified	Uncertain significance (Nov 12, 2021)
1-86473873-C-A		not specified	Uncertain significance (Feb 17, 2024)
1-86476494-T-A		not specified	Uncertain significance (Jun 23, 2023)
1-86482267-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-86482273-G-T		not specified	Uncertain significance (Apr 28, 2023)
1-86482373-T-A		not specified	Uncertain significance (May 26, 2022)
1-86482378-A-G		not specified	Uncertain significance (Oct 24, 2023)
1-86486539-T-C		not specified	Uncertain significance (Sep 13, 2023)
1-86486614-C-T		not specified	Uncertain significance (Feb 10, 2022)
1-86486743-C-T		not specified	Uncertain significance (Oct 31, 2023)
1-86489026-T-C		not specified	Uncertain significance (Dec 28, 2022)
1-86489060-A-G		not specified	Uncertain significance (Aug 14, 2023)
1-86489135-C-T		not specified	Uncertain significance (Apr 05, 2023)
1-86491267-G-C		not specified	Uncertain significance (Feb 03, 2022)
1-86491360-C-T		not specified	Uncertain significance (Jan 24, 2023)
1-86493436-T-A		not specified	Uncertain significance (Jul 12, 2023)
1-86493466-C-G		not specified	Uncertain significance (Jan 22, 2024)
1-86493546-G-T		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLCA1	protein_coding	protein_coding	ENST00000234701	14	31922

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.28e-9	0.999	125641	0	107	125748	0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.705	449	493	0.911	0.0000253	5973
Missense in Polyphen		154	187.4	0.82176		2316
Synonymous	-0.554	194	184	1.05	0.0000101	1813
Loss of Function	2.99	21	41.9	0.501	0.00000233	471

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00116	0.00116
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.000220	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000391	0.000387
Middle Eastern	0.000220	0.000217
South Asian	0.000527	0.000523
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in mediating calcium-activated chloride conductance. May play critical roles in goblet cell metaplasia, mucus hypersecretion, cystic fibrosis and AHR. May be involved in the regulation of mucus production and/or secretion by goblet cells. Involved in the regulation of tissue inflammation in the innate immune response. May play a role as a tumor suppressor. Induces MUC5AC. {ECO:0000269|PubMed:11445004, ECO:0000269|PubMed:11842292, ECO:0000269|PubMed:11956057, ECO:0000269|PubMed:23112050, ECO:0000269|PubMed:9828122}.
• Pathway: Renin secretion - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Stimuli-sensing channels;Ion channel transport;Alpha6Beta4Integrin;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.827
• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.66

Haploinsufficiency Scores

• pHI: 0.0452
• hipred: N
• hipred_score: 0.350

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.542

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clca1
• Phenotype: homeostasis/metabolism phenotype; respiratory system phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: proteolysis;calcium ion transport;ion transmembrane transport;cellular response to hypoxia;chloride transmembrane transport
• Cellular component: extracellular space;plasma membrane;integral component of plasma membrane;microvillus;zymogen granule membrane
• Molecular function: metalloendopeptidase activity;intracellular calcium activated chloride channel activity;chloride channel activity;metal ion binding