CLCA2
geneOn this page
Also known as CLCRG2
Summary
CLCA2 (chloride channel accessory 2, HGNC:2016) is a protein-coding gene on chromosome 1p22.3, encoding Calcium-activated chloride channel regulator 2 (Q9UQC9). Plays a role in modulating chloride current across the plasma membrane in a calcium-dependent manner, and cell adhesion.
This gene encodes a member of the calcium-activated chloride channel regulator (CLCR) family of proteins. Members of this family regulate the transport of chloride across the plasma membrane. The encoded protein is autoproteolytically processed to generate N- and C- terminal fragments. Expression of this gene is upregulated by the tumor suppressor protein p53 in response to DNA damage. In breast cancer, expression of this gene is downregulated and the encoded protein may inhibit migration and invasion while promoting mesenchymal-to-epithelial transition in cancer cell lines.
Source: NCBI Gene 9635 — RefSeq curated summary.
At a glance
- Gene–disease (curated): heart conduction disease (Moderate, GenCC)
- GWAS associations: 3
- Clinical variants (ClinVar): 161 total
- Druggable target: yes
- MANE Select transcript:
NM_006536
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:2016 |
| Approved symbol | CLCA2 |
| Name | chloride channel accessory 2 |
| Location | 1p22.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | CLCRG2 |
| Ensembl gene | ENSG00000137975 |
| Ensembl biotype | protein_coding |
| OMIM | 604003 |
| Entrez | 9635 |
Gene structure
Transcript identifiers
Ensembl transcripts: 3 — 2 protein_coding_CDS_not_defined, 1 protein_coding
ENST00000370565, ENST00000490884, ENST00000498802
RefSeq mRNA: 1 — MANE Select: NM_006536
NM_006536
CCDS: CCDS708
Canonical transcript exons
ENST00000370565 — 14 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000932057 | 86447508 | 86447778 |
| ENSE00000932060 | 86440148 | 86440325 |
| ENSE00000932061 | 86438876 | 86439106 |
| ENSE00000932062 | 86434518 | 86434745 |
| ENSE00000932063 | 86432369 | 86432528 |
| ENSE00000932065 | 86428418 | 86428568 |
| ENSE00000932066 | 86425339 | 86425476 |
| ENSE00001186623 | 86430862 | 86430970 |
| ENSE00001453032 | 86455085 | 86456553 |
| ENSE00001453033 | 86424171 | 86424433 |
| ENSE00003589179 | 86453369 | 86453602 |
| ENSE00003601334 | 86441437 | 86441543 |
| ENSE00003658828 | 86450563 | 86450733 |
| ENSE00003683749 | 86443787 | 86444011 |
Expression profiles
Bgee: expression breadth ubiquitous, 176 present calls, max score 99.58.
FANTOM5 (CAGE): breadth broad, TPM avg 5.7085 / max 1020.3016, expressed in 242 samples.
FANTOM5 promoters (5 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 3845 | 3.1574 | 130 |
| 3844 | 1.7545 | 148 |
| 3843 | 0.3997 | 113 |
| 3842 | 0.2508 | 59 |
| 3846 | 0.1461 | 43 |
Top tissues by expression
273 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| gingival epithelium | UBERON:0001949 | 99.58 | gold quality |
| gingiva | UBERON:0001828 | 99.49 | gold quality |
| tongue squamous epithelium | UBERON:0006919 | 98.88 | gold quality |
| penis | UBERON:0000989 | 98.74 | gold quality |
| upper leg skin | UBERON:0004262 | 98.58 | gold quality |
| mammalian vulva | UBERON:0000997 | 98.56 | gold quality |
| squamous epithelium | UBERON:0006914 | 98.36 | gold quality |
| oral cavity | UBERON:0000167 | 98.29 | gold quality |
| esophagus squamous epithelium | UBERON:0006920 | 97.99 | gold quality |
| hair follicle | UBERON:0002073 | 97.87 | gold quality |
| upper arm skin | UBERON:0004263 | 97.83 | gold quality |
| cervix squamous epithelium | UBERON:0006922 | 97.81 | gold quality |
| cervix epithelium | UBERON:0004801 | 97.72 | gold quality |
| epithelium of esophagus | UBERON:0001976 | 97.44 | gold quality |
| bronchial epithelial cell | CL:0002328 | 97.35 | gold quality |
| esophagus mucosa | UBERON:0002469 | 96.61 | gold quality |
| skin of hip | UBERON:0001554 | 96.58 | gold quality |
| pharyngeal mucosa | UBERON:0000355 | 96.57 | gold quality |
| epithelium of bronchus | UBERON:0002031 | 95.75 | gold quality |
| bronchus | UBERON:0002185 | 94.79 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 93.96 | gold quality |
| olfactory segment of nasal mucosa | UBERON:0005386 | 93.51 | gold quality |
| body of tongue | UBERON:0011876 | 92.68 | gold quality |
| zone of skin | UBERON:0000014 | 92.67 | gold quality |
| skin of abdomen | UBERON:0001416 | 92.41 | gold quality |
| epithelium of nasopharynx | UBERON:0001951 | 92.22 | gold quality |
| skin of leg | UBERON:0001511 | 91.44 | gold quality |
| nipple | UBERON:0002030 | 90.71 | gold quality |
| tongue | UBERON:0001723 | 88.76 | gold quality |
| nasal cavity mucosa | UBERON:0001826 | 88.10 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 2.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-CURD-114 | yes | 185.47 |
| E-ANND-3 | yes | 16.84 |
Regulation
Is transcription factor: no
Upstream regulators (CollecTRI, top): GLI1, TP53
miRNA regulators (miRDB)
64 targeting CLCA2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-5011-5P | 100.00 | 83.46 | 5820 |
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-9-5P | 100.00 | 72.28 | 2361 |
| HSA-MIR-1277-5P | 100.00 | 73.95 | 5056 |
| HSA-MIR-4795-3P | 100.00 | 74.62 | 4024 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-4534 | 99.99 | 66.58 | 1907 |
| HSA-MIR-4531 | 99.99 | 69.70 | 3181 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-3692-3P | 99.98 | 70.27 | 2139 |
| HSA-MIR-548AN | 99.97 | 70.91 | 2817 |
| HSA-MIR-5688 | 99.96 | 73.23 | 4504 |
| HSA-MIR-495-3P | 99.96 | 72.81 | 4197 |
| HSA-MIR-8082 | 99.95 | 67.27 | 1170 |
| HSA-LET-7C-3P | 99.95 | 73.42 | 2862 |
| HSA-MIR-3910 | 99.95 | 71.13 | 2227 |
| HSA-MIR-552-5P | 99.93 | 68.56 | 1583 |
| HSA-MIR-7-1-3P | 99.91 | 71.53 | 4384 |
| HSA-MIR-7-2-3P | 99.91 | 71.40 | 4394 |
| HSA-MIR-627-3P | 99.90 | 71.42 | 3316 |
| HSA-MIR-95-5P | 99.89 | 72.17 | 3973 |
| HSA-MIR-10395-5P | 99.86 | 67.35 | 676 |
| HSA-MIR-5582-3P | 99.86 | 72.48 | 4221 |
| HSA-MIR-548AR-3P | 99.85 | 71.26 | 3889 |
| HSA-MIR-6875-3P | 99.82 | 70.26 | 2983 |
| HSA-MIR-548AZ-3P | 99.82 | 70.56 | 3549 |
| HSA-MIR-548BC | 99.82 | 70.61 | 3524 |
| HSA-MIR-548E-3P | 99.82 | 70.59 | 3514 |
| HSA-MIR-548F-3P | 99.82 | 70.59 | 3540 |
| HSA-MIR-374C-5P | 99.80 | 72.06 | 2910 |
Literature-anchored findings (GeneRIF, showing 22)
- Expression of hSK4 as well as hCACC-2 and hCACC-3 but not hCACC-1 was demonstrated by reverse transcriptase PCR on native nasal tissues. (PMID:12612194)
- immunohistochemistry clearly demonstrated colocalisation between hCLCA2 and integrin beta4 (PMID:15707651)
- human CLCA2 protein and mRNA expression are elevated during epithelial stratification, suggesting that this protein plays a role in the growth of multi-layered corneal epithelia during both natural development and tissue cultivation. (PMID:16158324)
- Mostly extracellular with only a single transmembrane segment, unlikely to form a channel. (PMID:16873362)
- hCLCA2 Is a p53-Inducible Inhibitor of Breast Cancer Cell Proliferation. (PMID:19654313)
- hCLCA2 is required for epithelial differentiation, and its loss during tumor progression contributes to metastasis. (PMID:21909135)
- the reduced expression of CLCA2 was frequently observed in various kinds of cancers including prostate cancer (PMID:22431922)
- These results strongly suggest that CLCA2 is involved in the p53 tumor suppressor network and has a significant effect on cell migration and invasion. (PMID:22990203)
- CLCA2 expression is higher in squamous cell carcinoma of the lung compared with adenocarcinoma. (PMID:25548429)
- Variants in CLCA2 were associated with an ileal involvement phenotype of Crohn’s disease. (PMID:25557950)
- CLCA2 links junctional adhesion molecule EVA1, to cytosolic signaling proteins that modulate proliferation and differentiation. (PMID:26930581)
- CLCA2 suppress NPC proliferation, migration, invasion and epithelial-mesenchymal transition through inhibiting FAK/ERK signaling. (PMID:29463274)
- identified a new molecular mechanism to explain PCa and MeS link based on CLCA2 repression by CTBP1 and miR-196b-5p molecules that might act as key factors in the progression onset of this disease (PMID:29536528)
- CLCA2 knockdown promoted keratinocyte apoptosis induced by hyperosmotic stress through impairment of cell-cell adhesion. (PMID:29743348)
- we found by calcium imaging that CLCA2 moderately enhanced intracellular-store release but dramatically increased store-operated entry of calcium upon cytosolic depletion (PMID:29758025)
- A novel heterozygous missense mutation c.G1725T of the CLCA2 gene may be associated with heart block disease. (PMID:31326550)
- Genome-wide meta-analysis identified novel variant associated with hallux valgus in Caucasians. (PMID:32131869)
- CLCA2 was identified as a potential prognostic marker for triple negative breast cancer in African American women. (PMID:32298355)
- Decreased expression of CLCA2 and the correlating with immune infiltrates in patients with cervical squamous cell carcinoma: A bioinformatics analysis. (PMID:33966732)
- CLCA2 overexpression suppresses epithelial-to-mesenchymal transition in cervical cancer cells through inactivation of ERK/JNK/p38-MAPK signaling pathways. (PMID:36280802)
- TP63 truncating mutation causes increased cell apoptosis and premature ovarian insufficiency by enhanced transcriptional activation of CLCA2. (PMID:38528613)
- Transport of CLCA2 to the nucleus by extracellular vesicles controls keratinocyte survival and migration. (PMID:38602325)
Cross-species orthologs
2 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Clca2 | ENSMUSG00000036960 |
| rattus_norvegicus | Clca2 | ENSRNOG00000013771 |
Paralogs (2): CLCA1 (ENSG00000016490), CLCA4 (ENSG00000016602)
Protein
Protein identifiers
Calcium-activated chloride channel regulator 2 — Q9UQC9 (reviewed: Q9UQC9)
Alternative names: Calcium-activated chloride channel family member 2, Calcium-activated chloride channel protein 3
All UniProt accessions (1): Q9UQC9
UniProt curated annotations — full annotation on UniProt →
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.
Subcellular location. Cell membrane. Basal cell membrane. Cell junction Secreted.
Tissue specificity. Expressed in cornea, skin, vagina, esophagus, and larynx (at protein level). Expressed in trachea and mammary gland. Weakly expressed in testis and kidney. Highly expressed in corneal epithelium, colon and trachea. Moderately expressed in brain, urogenital organs, bladder, uterus and prostate. Highly expressed in tissues containing stratified epithelium including cornea, esophagus, larynx, skin and vagina than those tissues which contain only epithelial monolayers. Expressed in normal breast epithelium but not in breast cancer. Highly expressed during epithelial stratification. Expressed in endothelial cells of lung. Expressed selectively in endothelia of small pulmonary arteries, arterioles, and subpleural and interlobular venules.
Post-translational modifications. The 141 kDa mature form is autoproteolytically cleaved by the metalloprotease domain, producing a 109 kDa form and a 35 kDa form. The cleavage is necessary for calcium-activated chloride channel (CaCC) activation activity. N-glycosylated.
Domain organisation. The metalloprotease region is responsible for autoproteolytic processing. It can also cross-cleave other CLCA substrates.
Induction. Significantly down-regulated in breast and colorectal cancer.
Similarity. Belongs to the CLCR family.
RefSeq proteins (1): NP_006527* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR002035 | VWF_A | Domain |
| IPR004727 | CLCA_chordata | Family |
| IPR013642 | CLCA_N | Domain |
| IPR036465 | vWFA_dom_sf | Homologous_superfamily |
| IPR051266 | CLCR | Family |
Pfam: PF08434
UniProt features (31 total): mutagenesis site 6, glycosylation site 5, sequence variant 4, chain 3, binding site 3, sequence conflict 2, topological domain 2, signal peptide 1, site 1, transmembrane region 1, domain 1, region of interest 1, active site 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9UQC9-F1 | 86.87 | 0.65 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Catalytic / active sites (2): 708–709 (cleavage; by autolysis); 165
Ligand- & substrate-binding residues (3): 164; 168; 175
Glycosylation sites (5): 74, 150, 231, 522, 822
Mutagenesis-validated functional residues (6):
| Position | Phenotype |
|---|---|
| 150 | reduction in size by around 2 kda. |
| 292 | no change in size. |
| 522 | reduction in size by around 2 kda. |
| 637 | no change in size. |
| 822 | reduction in size by around 2 kda. |
| 938 | no change in size. |
Function
Pathways and Gene Ontology
Reactome pathways
1 pathways
| ID | Pathway |
|---|---|
| R-HSA-2672351 | Stimuli-sensing channels |
MSigDB gene sets: 117 (showing top):
GOMF_METALLOPEPTIDASE_ACTIVITY, JAEGER_METASTASIS_DN, GOBP_INORGANIC_ANION_TRANSPORT, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, GOBP_CHLORIDE_TRANSPORT, CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP, HUPER_BREAST_BASAL_VS_LUMINAL_UP, MODULE_99, KEGG_OLFACTORY_TRANSDUCTION, BECKER_TAMOXIFEN_RESISTANCE_DN, chr1p22, RIGGI_EWING_SARCOMA_PROGENITOR_UP, GOBP_TRANSMEMBRANE_TRANSPORT, HOWLIN_CITED1_TARGETS_1_DN, DOANE_BREAST_CANCER_CLASSES_UP
GO Biological Process (6): proteolysis (GO:0006508), cell adhesion (GO:0007155), monoatomic ion transmembrane transport (GO:0034220), monoatomic ion transport (GO:0006811), chloride transport (GO:0006821), chloride transmembrane transport (GO:1902476)
GO Molecular Function (8): metalloendopeptidase activity (GO:0004222), intracellularly calcium-gated chloride channel activity (GO:0005229), chloride channel activity (GO:0005254), metal ion binding (GO:0046872), peptidase activity (GO:0008233), metallopeptidase activity (GO:0008237), ligand-gated monoatomic ion channel activity (GO:0015276), hydrolase activity (GO:0016787)
GO Cellular Component (9): extracellular region (GO:0005576), nucleoplasm (GO:0005654), cytosol (GO:0005829), plasma membrane (GO:0005886), basal plasma membrane (GO:0009925), cell junction (GO:0030054), nuclear membrane (GO:0031965), anchoring junction (GO:0070161), membrane (GO:0016020)
Reactome top-level categories
Rollup of top-1 pathways:
| Category | Pathways |
|---|---|
| Ion channel transport | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 5 |
| protein metabolic process | 1 |
| cellular process | 1 |
| monoatomic ion transport | 1 |
| transmembrane transport | 1 |
| transport | 1 |
| monoatomic anion transport | 1 |
| inorganic anion transport | 1 |
| chloride transport | 1 |
| monoatomic anion transmembrane transport | 1 |
| endopeptidase activity | 1 |
| metallopeptidase activity | 1 |
| chloride channel activity | 1 |
| ligand-gated monoatomic anion channel activity | 1 |
| intracellularly calcium-gated channel activity | 1 |
| monoatomic anion channel activity | 1 |
| chloride transmembrane transporter activity | 1 |
| cation binding | 1 |
| hydrolase activity | 1 |
| catalytic activity, acting on a protein | 1 |
| peptidase activity | 1 |
| monoatomic ion channel activity | 1 |
| ligand-gated channel activity | 1 |
| catalytic activity | 1 |
| nuclear lumen | 1 |
| cytoplasm | 1 |
| membrane | 1 |
| cell periphery | 1 |
| basal part of cell | 1 |
| plasma membrane region | 1 |
| nucleus | 1 |
| nuclear envelope | 1 |
| organelle membrane | 1 |
| cell junction | 1 |
Protein interactions and networks
STRING
1549 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| CLCA2 | ANO2 | Q9NQ90 | 973 |
| CLCA2 | ANO1 | Q5XXA6 | 925 |
| CLCA2 | CFTR | P13569 | 817 |
| CLCA2 | ANO6 | Q4KMQ2 | 657 |
| CLCA2 | ITGB4 | P16144 | 631 |
| CLCA2 | ANO10 | Q9NW15 | 602 |
| CLCA2 | BEST1 | O76090 | 598 |
| CLCA2 | BEST2 | Q8NFU1 | 589 |
| CLCA2 | LRRC8B | Q6P9F7 | 550 |
| CLCA2 | ANO5 | Q75V66 | 546 |
| CLCA2 | CLCN3 | P51790 | 533 |
| CLCA2 | SLC12A2 | P55011 | 481 |
| CLCA2 | LRRC8A | Q8IWT6 | 480 |
| CLCA2 | ANO7 | Q6IWH7 | 480 |
| CLCA2 | ANO9 | A1A5B4 | 479 |
IntAct
4 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| CLCA2 | H2BC12L | psi-mi:“MI:0915”(physical association) | 0.400 |
| CLCA2 | NDC1 | psi-mi:“MI:0915”(physical association) | 0.400 |
| ALB | CNOT1 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (6): RPS21 (Co-fractionation), NDC1 (Affinity Capture-MS), CLCA2 (Affinity Capture-MS), CLCA2 (Proximity Label-MS), SLC3A2 (Cross-Linking-MS (XL-MS)), CLCA2 (Affinity Capture-MS)
ESM2 similar proteins: A0A0B5GR44, A0A0D3QS97, A1L314, A4IH88, A7MCS3, B9DFR3, E7F0Z8, F4I107, F4I839, O35298, O54728, O80731, P38566, P38567, P38568, P70683, Q03311, Q0P6H9, Q3TTY0, Q3UUQ7, Q3V5L5, Q4V398, Q5GF25, Q5RBP9, Q60963, Q66GM8, Q6DBP4, Q6E279, Q6NQ51, Q75T13, Q765A7, Q765H6, Q812F3, Q84JS1, Q84WF0, Q8BG22, Q8BXJ9, Q8N2E2, Q93ZR8, Q940J8
Diamond homologs: A8K7I4, P54281, Q14CN2, Q2TU62, Q6PT52, Q6Q473, Q8BG22, Q9D7Z6, Q9QX15, Q9TUB5, Q9UQC9, Q55874
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
161 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 143 |
| Likely benign | 11 |
| Benign | 3 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
1851 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 1:86430860:A:AG | acceptor_gain | 1.0000 |
| 1:86430861:G:GG | acceptor_gain | 1.0000 |
| 1:86430967:CAAGG:C | donor_loss | 1.0000 |
| 1:86430968:AAGGT:A | donor_loss | 1.0000 |
| 1:86430969:AGGTT:A | donor_loss | 1.0000 |
| 1:86430971:G:GC | donor_loss | 1.0000 |
| 1:86432368:GGT:G | acceptor_gain | 1.0000 |
| 1:86432529:G:GG | donor_gain | 1.0000 |
| 1:86434512:TTCCA:T | acceptor_loss | 1.0000 |
| 1:86434513:TCCA:T | acceptor_loss | 1.0000 |
| 1:86434514:CCA:C | acceptor_loss | 1.0000 |
| 1:86434516:A:T | acceptor_loss | 1.0000 |
| 1:86434516:AGGT:A | acceptor_gain | 1.0000 |
| 1:86434517:GGT:G | acceptor_gain | 1.0000 |
| 1:86434517:GGTG:G | acceptor_gain | 1.0000 |
| 1:86434602:G:GT | donor_gain | 1.0000 |
| 1:86438866:T:TA | acceptor_gain | 1.0000 |
| 1:86438867:G:A | acceptor_gain | 1.0000 |
| 1:86438871:CATAG:C | acceptor_loss | 1.0000 |
| 1:86438873:TA:T | acceptor_loss | 1.0000 |
| 1:86438977:A:T | donor_gain | 1.0000 |
| 1:86439022:A:T | donor_gain | 1.0000 |
| 1:86439087:GGCT:G | donor_gain | 1.0000 |
| 1:86439099:GATT:G | donor_gain | 1.0000 |
| 1:86443784:CA:C | acceptor_loss | 1.0000 |
| 1:86443785:A:AG | acceptor_gain | 1.0000 |
| 1:86443785:AGCTT:A | acceptor_gain | 1.0000 |
| 1:86443786:G:GG | acceptor_gain | 1.0000 |
| 1:86443786:GC:G | acceptor_gain | 1.0000 |
| 1:86443786:GCT:G | acceptor_gain | 1.0000 |
AlphaMissense
6228 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 1:86430882:T:A | W166R | 0.990 |
| 1:86430882:T:C | W166R | 0.990 |
| 1:86453566:T:A | W785R | 0.982 |
| 1:86453566:T:C | W785R | 0.982 |
| 1:86430897:T:A | W171R | 0.977 |
| 1:86430897:T:C | W171R | 0.977 |
| 1:86432460:T:A | C226S | 0.966 |
| 1:86432461:G:C | C226S | 0.966 |
| 1:86434581:T:A | C270S | 0.963 |
| 1:86434582:G:C | C270S | 0.963 |
| 1:86425354:G:C | A68P | 0.962 |
| 1:86447670:G:C | A626P | 0.961 |
| 1:86447713:T:A | V640D | 0.959 |
| 1:86425367:T:C | L72P | 0.957 |
| 1:86430892:T:C | L169P | 0.957 |
| 1:86430885:G:C | A167P | 0.956 |
| 1:86447517:T:A | W575R | 0.956 |
| 1:86447517:T:C | W575R | 0.956 |
| 1:86430895:G:C | R170P | 0.953 |
| 1:86432370:T:C | C196R | 0.948 |
| 1:86432460:T:C | C226R | 0.948 |
| 1:86455288:G:C | A865P | 0.947 |
| 1:86430899:G:C | W171C | 0.946 |
| 1:86430899:G:T | W171C | 0.946 |
| 1:86434527:T:C | F252L | 0.946 |
| 1:86434529:T:A | F252L | 0.946 |
| 1:86434529:T:G | F252L | 0.946 |
| 1:86447718:G:C | A642P | 0.945 |
| 1:86447719:C:A | A642D | 0.944 |
| 1:86430884:G:C | W166C | 0.943 |
dbSNP variants (sampled 300 via entrez): RS1000000026 (1:86436240 G>A,C), RS1000302300 (1:86448321 G>A), RS1000386797 (1:86454800 CAAAACAAAAACA>C,CAAAACA,CAAAACAAAAACAAAAACA), RS1000411676 (1:86448047 C>A,G), RS1000447097 (1:86442100 A>G), RS1000471269 (1:86437042 G>C), RS1000496415 (1:86431499 C>G), RS1000502385 (1:86436593 G>A), RS1000511046 (1:86441239 A>G), RS1000632187 (1:86431871 G>T), RS1000696880 (1:86425167 GT>G,GTT), RS1000819260 (1:86447269 G>A), RS1000886646 (1:86448748 T>A,G), RS1000895859 (1:86443258 A>G), RS1000904487 (1:86449675 G>A,C)
Disease associations
OMIM: gene MIM:604003 | disease phenotypes:
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| heart conduction disease | Moderate | Autosomal dominant |
Mondo (1): heart conduction disease (MONDO:0000992)
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
3 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST002729_3 | Crohn’s disease-related phenotypes | 1.000000e-06 |
| GCST009847_1 | Hallux valgus | 3.000000e-09 |
| GCST009849_2 | Hallux valgus | 2.000000e-06 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: yes
ChEMBL targets (1): CHEMBL2364708 (PROTEIN FAMILY)
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
34 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| sodium arsenite | decreases expression, increases expression | 3 |
| Benzo(a)pyrene | increases expression, increases mutagenesis | 3 |
| Formaldehyde | decreases expression, increases expression | 2 |
| Tobacco Smoke Pollution | decreases expression | 2 |
| lead acetate | decreases expression | 1 |
| 2,5,2’,5’-tetrachlorobiphenyl | decreases expression | 1 |
| terbufos | increases methylation | 1 |
| perfluorooctanoic acid | increases expression | 1 |
| zinc chromate | increases abundance, increases expression | 1 |
| cupric chloride | decreases expression | 1 |
| S-(1,2-dichlorovinyl)cysteine | affects response to substance, increases expression, affects cotreatment | 1 |
| chromium hexavalent ion | increases abundance, increases expression | 1 |
| perfluorooctane sulfonic acid | decreases expression | 1 |
| perfluorohexanesulfonic acid | increases expression | 1 |
| nutlin 3 | affects cotreatment, increases expression | 1 |
| jinfukang | affects cotreatment, increases expression | 1 |
| incobotulinumtoxinA | increases expression | 1 |
| Arsenic Trioxide | increases expression | 1 |
| Air Pollutants | decreases expression, increases abundance | 1 |
| Cadmium | increases expression | 1 |
| Cisplatin | affects cotreatment, increases expression | 1 |
| Dactinomycin | increases expression, affects cotreatment | 1 |
| Fonofos | increases methylation | 1 |
| Estradiol | affects cotreatment, decreases expression | 1 |
| Ethyl Methanesulfonate | increases expression | 1 |
| Lipopolysaccharides | affects response to substance, increases expression, affects cotreatment | 1 |
| Lucanthone | increases expression | 1 |
| Methyl Methanesulfonate | increases expression | 1 |
| Parathion | increases methylation | 1 |
| Vanadates | increases expression | 1 |
Cellosaurus cell lines
1 cell lines: 1 transformed cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_E7X0 | HEK-293 hCLCA2 | Transformed cell line | Female |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Associated diseases: heart conduction disease
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): heart conduction disease, ileocolitis