CLCA2

chloride channel accessory 2, the group of Chloride channel accessory

Basic information

Region (hg38): 1:86424171-86456553

Links

ENSG00000137975

∙ NCBI:9635 ∙ OMIM:604003 ∙ HGNC:2016 ∙ Uniprot:Q9UQC9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

heart conduction disease (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLCA2 gene.

not_specified (130 variants)
not_provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLCA2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006536.7. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	2 clinvar	4
missense			125 clinvar	8 clinvar		133
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	125	10	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLCA2	protein_coding	protein_coding	ENST00000370565	14	32473

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.47e-28	0.000138	125577	1	170	125748	0.000680

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.373	469	492	0.953	0.0000236	6191
Missense in Polyphen		139	160.23	0.8675		2086
Synonymous	-1.76	204	174	1.17	0.00000840	1819
Loss of Function	0.0804	43	43.6	0.987	0.00000254	490

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00161	0.00161
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000381	0.000381
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000867	0.000862
Middle Eastern	0.000381	0.000381
South Asian	0.000790	0.000752
Other	0.000658	0.000652

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays a role in modulating chloride current across the plasma membrane in a calcium-dependent manner, and cell adhesion. Involved in basal cell adhesion and/or stratification of squamous epithelia. May act as a tumor suppressor in breast and colorectal cancer. Plays a key role for cell adhesion in the beginning stages of lung metastasis via the binding to ITGB4. {ECO:0000269|PubMed:10554024, ECO:0000269|PubMed:11320086, ECO:0000269|PubMed:11445004, ECO:0000269|PubMed:15707651, ECO:0000269|PubMed:16158324}.;
Pathway: Renin secretion - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Stimuli-sensing channels;Ion channel transport;p73 transcription factor network;Transport of small molecules;Validated transcriptional targets of TAp63 isoforms (Consensus)

Recessive Scores

pRec: 0.157

Intolerance Scores

loftool: 0.966
rvis_EVS: -0.04
rvis_percentile_EVS: 50.54

Haploinsufficiency Scores

pHI: 0.178
hipred: N
hipred_score: 0.153
ghis: 0.471

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0361

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Clca2
Phenotype: liver/biliary system phenotype;

Gene ontology

Biological process: proteolysis;cell adhesion;ion transmembrane transport;chloride transmembrane transport
Cellular component: extracellular region;nucleus;cytosol;plasma membrane;integral component of plasma membrane;basal plasma membrane;cell junction;nuclear membrane
Molecular function: metalloendopeptidase activity;intracellular calcium activated chloride channel activity;chloride channel activity;ligand-gated ion channel activity;metal ion binding