CDHR5
gene geneOn this page
Also known as FLJ20219MU-PCDH
Summary
CDHR5 (cadherin related family member 5, HGNC:7521) is a protein-coding gene on chromosome 11p15.5, encoding Cadherin-related family member 5 (Q9HBB8). Intermicrovillar adhesion molecule that forms, via its extracellular domain, calcium-dependent heterophilic complexes with CDHR2 on adjacent microvilli.
This gene is a novel mucin-like gene that is a member of the cadherin superfamily. While encoding nonpolymorphic tandem repeats rich in proline, serine and threonine similar to mucin proteins, the gene also contains sequence encoding calcium-binding motifs found in all cadherins. The role of the hybrid extracellular region and the specific function of this protein have not yet been determined. Alternatively spliced transcript variants encoding different isoforms have been described.
Source: NCBI Gene 53841 — RefSeq curated summary.
At a glance
- GWAS associations: 2
- Clinical variants (ClinVar): 221 total
- MANE Select transcript:
NM_021924
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:7521 |
| Approved symbol | CDHR5 |
| Name | cadherin related family member 5 |
| Location | 11p15.5 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ20219, MU-PCDH |
| Ensembl gene | ENSG00000099834 |
| Ensembl biotype | protein_coding |
| OMIM | 606839 |
| Entrez | 53841 |
Gene structure
Transcript identifiers
Ensembl transcripts: 35 — 31 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron
ENST00000349570, ENST00000358353, ENST00000397542, ENST00000526077, ENST00000529337, ENST00000531088, ENST00000531177, ENST00000531899, ENST00000532949, ENST00000534311, ENST00000674088, ENST00000872864, ENST00000872865, ENST00000872866, ENST00000872867, ENST00000872868, ENST00000872869, ENST00000872870, ENST00000872871, ENST00000872872, ENST00000872873, ENST00000872874, ENST00000872875, ENST00000872876, ENST00000872877, ENST00000872878, ENST00000872879, ENST00000872880, ENST00000872881, ENST00000872882, ENST00000872883, ENST00000872884, ENST00000954966, ENST00000954967, ENST00000954968
RefSeq mRNA: 3 — MANE Select: NM_021924
NM_001171968, NM_021924, NM_031264
CCDS: CCDS7707, CCDS7708, CCDS91397
Canonical transcript exons
ENST00000397542 — 15 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001529139 | 616583 | 617770 |
| ENSE00003462077 | 617954 | 618111 |
| ENSE00003481439 | 619306 | 619390 |
| ENSE00003529989 | 621080 | 621250 |
| ENSE00003533200 | 620296 | 620386 |
| ENSE00003540790 | 621562 | 621663 |
| ENSE00003541979 | 624818 | 624955 |
| ENSE00003543780 | 621812 | 621904 |
| ENSE00003554698 | 624557 | 624732 |
| ENSE00003566387 | 619474 | 619587 |
| ENSE00003569169 | 620067 | 620164 |
| ENSE00003585889 | 621345 | 621455 |
| ENSE00003631793 | 624213 | 624263 |
| ENSE00003662113 | 619681 | 619881 |
| ENSE00003672988 | 618599 | 619180 |
Expression profiles
Bgee: expression breadth ubiquitous, 132 present calls, max score 99.50.
FANTOM5 (CAGE): breadth tissue_specific, TPM avg 5.5208 / max 2850.6252, expressed in 98 samples.
FANTOM5 promoters (7 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 117798 | 5.3199 | 67 |
| 117794 | 0.1246 | 35 |
| 117793 | 0.0213 | 11 |
| 117791 | 0.0180 | 6 |
| 117792 | 0.0179 | 10 |
| 206073 | 0.0097 | 6 |
| 117799 | 0.0093 | 7 |
Top tissues by expression
133 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| duodenum | UBERON:0002114 | 99.50 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 98.75 | gold quality |
| rectum | UBERON:0001052 | 98.13 | gold quality |
| right lobe of liver | UBERON:0001114 | 97.32 | gold quality |
| liver | UBERON:0002107 | 97.06 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 93.96 | gold quality |
| small intestine | UBERON:0002108 | 93.71 | gold quality |
| adult mammalian kidney | UBERON:0000082 | 91.37 | gold quality |
| transverse colon | UBERON:0001157 | 91.28 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 88.50 | silver quality |
| kidney | UBERON:0002113 | 86.83 | gold quality |
| colonic epithelium | UBERON:0000397 | 84.20 | gold quality |
| intestine | UBERON:0000160 | 84.15 | gold quality |
| gall bladder | UBERON:0002110 | 83.07 | gold quality |
| sural nerve | UBERON:0015488 | 82.01 | gold quality |
| vermiform appendix | UBERON:0001154 | 80.85 | gold quality |
| colon | UBERON:0001155 | 80.38 | gold quality |
| cortex of kidney | UBERON:0001225 | 77.83 | gold quality |
| islet of Langerhans | UBERON:0000006 | 73.36 | gold quality |
| metanephros cortex | UBERON:0010533 | 72.89 | gold quality |
| stomach | UBERON:0000945 | 69.35 | gold quality |
| body of stomach | UBERON:0001161 | 68.89 | gold quality |
| bone marrow cell | CL:0002092 | 68.53 | silver quality |
| pancreas | UBERON:0001264 | 68.06 | gold quality |
| smooth muscle tissue | UBERON:0001135 | 66.64 | gold quality |
| fundus of stomach | UBERON:0001160 | 66.56 | gold quality |
| muscle layer of sigmoid colon | UBERON:0035805 | 64.95 | gold quality |
| body of pancreas | UBERON:0001150 | 64.55 | gold quality |
| adrenal tissue | UBERON:0018303 | 63.95 | gold quality |
| bone marrow | UBERON:0002371 | 63.57 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 2.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-125970 | yes | 30.17 |
| E-ANND-3 | yes | 15.99 |
Regulation
Is transcription factor: no
Upstream regulators (CollecTRI, top): HNF4A
miRNA regulators (miRDB)
14 targeting CDHR5, 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-6870-5P | 99.99 | 68.55 | 2115 |
| HSA-MIR-4723-5P | 99.97 | 68.70 | 2034 |
| HSA-MIR-5698 | 99.97 | 68.49 | 2029 |
| HSA-MIR-7111-5P | 99.97 | 68.48 | 2062 |
| HSA-MIR-623 | 99.76 | 68.16 | 1170 |
| HSA-MIR-4437 | 99.52 | 65.29 | 1266 |
| HSA-MIR-1275 | 99.47 | 67.90 | 2749 |
| HSA-MIR-3978 | 99.24 | 68.39 | 2201 |
| HSA-MIR-3199 | 99.17 | 65.19 | 696 |
| HSA-MIR-8052 | 99.17 | 65.01 | 719 |
| HSA-MIR-661 | 99.09 | 65.94 | 2062 |
| HSA-MIR-6827-5P | 98.46 | 64.88 | 1256 |
| HSA-MIR-3665 | 97.73 | 65.08 | 975 |
| HSA-MIR-376A-2-5P | 96.43 | 68.06 | 715 |
Literature-anchored findings (GeneRIF, showing 11)
- identifed the human mu-protocadherin ortholog and examined its expression in the developing kidney (PMID:12167596)
- MUCDHL genes are biallelically expressed in multiple fetal and adult tissues both in humans and in mice (PMID:12589428)
- Our data consequently suggest that down-regulation of mu-protocadherin expression is a common event in colorectal carcinogenesis and might therefore play an important role in this pathologic process. (PMID:21315419)
- The MUPCDH genetic polymorphism rs3758650 was considered a genetic marker to predict symptomatic Gallstone disease subjects. (PMID:21839066)
- The transcription factor Cdx2 activates expression of the protocadherin Mucdhl, which interacts with beta-catenin and regulates activities of colon cancer cells. (PMID:22202456)
- Study found that brush border assembly is driven by the formation of Ca(2+)-dependent adhesion links between adjacent microvilli. Intermicrovillar links are composed of protocadherin-24 and mucin-like protocadherin, which target to microvillar tips and interact to form a trans-heterophilic complex. (PMID:24725409)
- It suggests that methylation status of MUPCDH promoter can be used as a novel epigenetic biomarker and a therapeutic target in ADPKD. (PMID:26463459)
- Expression of MUCDHL is negatively regulated by the activation of the beta-catenin signaling pathway in normal and cancer colorectal enterocytes. (PMID:27310872)
- Up-regulation of CDHR5 expression promotes malignant phenotype of pancreatic ductal adenocarcinoma. (PMID:33025744)
- The atypical cadherin MUCDHL antagonizes colon cancer formation and inhibits oncogenic signaling through multiple mechanisms. (PMID:33188295)
- Heterophilic and homophilic cadherin interactions in intestinal intermicrovillar links are species dependent. (PMID:34871294)
Cross-species orthologs
2 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Cdhr5 | ENSMUSG00000025497 |
| rattus_norvegicus | Cdhr5 | ENSRNOG00000017762 |
Paralogs (33): CDH1 (ENSG00000039068), CDH10 (ENSG00000040731), CDH3 (ENSG00000062038), CDH19 (ENSG00000071991), CDHR2 (ENSG00000074276), CDH17 (ENSG00000079112), CDH7 (ENSG00000081138), PCDH11Y (ENSG00000099715), CDH20 (ENSG00000101542), PCDH11X (ENSG00000102290), CDH23 (ENSG00000107736), CDH9 (ENSG00000113100), CDH6 (ENSG00000113361), CDH26 (ENSG00000124215), CDHR3 (ENSG00000128536), CDH15 (ENSG00000129910), CDH24 (ENSG00000139880), CDH11 (ENSG00000140937), CDH13 (ENSG00000140945), CDH18 (ENSG00000145526), CDHR1 (ENSG00000148600), CDH22 (ENSG00000149654), CDH8 (ENSG00000150394), CDH12 (ENSG00000154162), PCDH1 (ENSG00000156453), DCHS1 (ENSG00000166341), PCDH7 (ENSG00000169851), CDH2 (ENSG00000170558), CDH4 (ENSG00000179242), CDH5 (ENSG00000179776), PCDH9 (ENSG00000184226), DCHS2 (ENSG00000197410), PCDH20 (ENSG00000280165)
Protein
Protein identifiers
Cadherin-related family member 5 — Q9HBB8 (reviewed: Q9HBB8)
Alternative names: Mu-protocadherin, Mucin and cadherin-like protein, Mucin-like protocadherin
All UniProt accessions (5): Q9HBB8, E9PKR2, E9PLX6, E9PMY2, E9PPW2
UniProt curated annotations — full annotation on UniProt →
Function. Intermicrovillar adhesion molecule that forms, via its extracellular domain, calcium-dependent heterophilic complexes with CDHR2 on adjacent microvilli. Thereby, controls the packing of microvilli at the apical membrane of epithelial cells. Through its cytoplasmic domain, interacts with microvillus cytoplasmic proteins to form the intermicrovillar adhesion complex/IMAC. This complex plays a central role in microvilli and epithelial brush border differentiation.
Subunit / interactions. Part of the IMAC/intermicrovillar adhesion complex/intermicrovillar tip-link complex composed of ANKS4B, MYO7B, USH1C, CDHR2 and CDHR5. Interacts (via cytoplasmic domain) with USH1C and MYO7B; required for proper localization of CDHR5 to microvilli tips and its function in brush border differentiation.
Subcellular location. Apical cell membrane. Cell projection. Microvillus membrane.
Tissue specificity. Highest expression in kidney, liver, colon and small intestine. In kidney, expressed apically along brush border of proximal convoluted tubule but not in cortical collecting ducts. Isoform 1 is expressed primarily in adult small intestine and colon. Isoform 2 is highly expressed in fetal liver. Expressed in duodenum with higher expression in enterocytes along the villus axis and lower expression in crypts (at protein level).
Post-translational modifications. N- and O-glycosylated.
Isoforms (3)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q9HBB8-1 | 1, MUCDHL-FL, MLPCDH-L | yes |
| Q9HBB8-2 | 2, MLPCDH-S | |
| Q9HBB8-4 | 3 |
RefSeq proteins (3): NP_001165439, NP_068743, NP_112554 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR002126 | Cadherin-like_dom | Domain |
| IPR015919 | Cadherin-like_sf | Homologous_superfamily |
| IPR020894 | Cadherin_CS | Conserved_site |
| IPR050174 | Protocadherin/Cadherin-CA | Family |
UniProt features (72 total): strand 14, glycosylation site 8, compositionally biased region 7, sequence conflict 6, region of interest 5, modified residue 5, sequence variant 5, repeat 4, domain 4, turn 3, topological domain 2, splice variant 2, mutagenesis site 2, helix 2, signal peptide 1, chain 1, transmembrane region 1
Structure
Experimental structures (PDB)
1 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 6OAE | X-RAY DIFFRACTION | 1.9 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9HBB8-F1 | 69.84 | 0.44 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Post-translational modifications (5): 770, 810, 817, 819, 821
Glycosylation sites (8): 44, 81, 140, 198, 297, 308, 405, 526
Mutagenesis-validated functional residues (2):
| Position | Phenotype |
|---|---|
| 109 | loss of binding to cdhr2. |
| 845 | loss of interaction with ush1c. |
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 102 (showing top):
GNF2_GSTM1, GNF2_HPN, TGACCTY_ERR1_Q2, CAGCTG_AP4_Q5, GOBP_CELL_CELL_ADHESION, GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_SIZE, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GNF2_LCAT, TCCCCAC_MIR491, HNF4_01, GNF2_HPX, SANSOM_APC_TARGETS_DN, GOCC_APICAL_PLASMA_MEMBRANE, GOBP_REGULATION_OF_MICROVILLUS_ORGANIZATION, SABATES_COLORECTAL_ADENOMA_DN
GO Biological Process (7): cell adhesion (GO:0007155), homophilic cell-cell adhesion (GO:0007156), cell differentiation (GO:0030154), regulation of microvillus length (GO:0032532), intermicrovillar adhesion (GO:0090675), cell-cell adhesion (GO:0098609), brush border assembly (GO:1904970)
GO Molecular Function (4): calcium ion binding (GO:0005509), beta-catenin binding (GO:0008013), cell adhesion molecule binding (GO:0050839), protein binding (GO:0005515)
GO Cellular Component (10): plasma membrane (GO:0005886), microvillus (GO:0005902), clathrin-coated pit (GO:0005905), apical plasma membrane (GO:0016324), brush border membrane (GO:0031526), microvillus membrane (GO:0031528), synapse (GO:0045202), extracellular exosome (GO:0070062), membrane (GO:0016020), cell projection (GO:0042995)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| protein binding | 2 |
| membrane | 2 |
| cell projection membrane | 2 |
| cellular anatomical structure | 2 |
| cellular process | 1 |
| cell-cell adhesion | 1 |
| cellular developmental process | 1 |
| regulation of microvillus organization | 1 |
| regulation of cell projection size | 1 |
| homotypic cell-cell adhesion | 1 |
| brush border assembly | 1 |
| cell adhesion | 1 |
| cellular component assembly | 1 |
| metal ion binding | 1 |
| binding | 1 |
| cell periphery | 1 |
| actin filament bundle | 1 |
| actin-based cell projection | 1 |
| endomembrane system | 1 |
| apical part of cell | 1 |
| plasma membrane region | 1 |
| brush border | 1 |
| apical plasma membrane | 1 |
| microvillus | 1 |
| cell junction | 1 |
| extracellular vesicle | 1 |
Protein interactions and networks
STRING
1028 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| CDHR5 | CDHR2 | Q9BYE9 | 991 |
| CDHR5 | E9PNW1 | E9PNW1 | 826 |
| CDHR5 | CDH17 | Q12864 | 814 |
| CDHR5 | ANKS4B | Q8N8V4 | 802 |
| CDHR5 | CDH23 | Q9H251 | 715 |
| CDHR5 | MYO7B | Q6PIF6 | 702 |
| CDHR5 | CTNNB1 | P35222 | 602 |
| CDHR5 | PCDH11X | Q9BZA7 | 520 |
| CDHR5 | LRRC57 | Q8N9N7 | 454 |
| CDHR5 | ESPN | B1AK53 | 451 |
| CDHR5 | WHRN | Q9P202 | 420 |
| CDHR5 | MYO1A | Q9UBC5 | 411 |
| CDHR5 | ARHGEF4 | Q9NR80 | 409 |
| CDHR5 | SLC25A22 | Q9H936 | 403 |
| CDHR5 | KHDRBS2 | Q5VWX1 | 400 |
| CDHR5 | CDX2 | Q99626 | 400 |
IntAct
6 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| USH1C | CDHR5 | psi-mi:“MI:0915”(physical association) | 0.520 |
| CDHR5 | MYO7B | psi-mi:“MI:0915”(physical association) | 0.400 |
| CDHR5 | LGALS1 | psi-mi:“MI:0914”(association) | 0.350 |
| CDHR2 | CDHR5 | psi-mi:“MI:0403”(colocalization) | 0.270 |
BioGRID (25): JMJD8 (Affinity Capture-MS), RETSAT (Affinity Capture-MS), MBLAC2 (Affinity Capture-MS), UFSP2 (Affinity Capture-MS), LGALS1 (Affinity Capture-MS), FITM2 (Affinity Capture-MS), XPO7 (Affinity Capture-MS), LEMD3 (Affinity Capture-MS), EFNB1 (Affinity Capture-MS), SORL1 (Affinity Capture-MS), CDHR5 (Proximity Label-MS), CDHR5 (Affinity Capture-RNA), CDHR5 (Affinity Capture-RNA), LEMD3 (Affinity Capture-MS), XPO7 (Affinity Capture-MS)
ESM2 similar proteins: A6NDA9, D3YX43, D5K8A9, O95256, P0CI71, P22272, P22273, P22934, P25118, P27930, P27931, P40967, P42703, P43121, P43303, Q00560, Q06154, Q149L7, Q29612, Q3SXY7, Q5RFR6, Q5SZV5, Q5VV43, Q60696, Q6PFC5, Q6UY09, Q7Z442, Q80ZD7, Q80ZD8, Q8IXH8, Q8IZA0, Q8K099, Q8K135, Q8MJS1, Q8N0Z9, Q8R2Y2, Q8R526, Q8VHF2, Q923P0, Q99650
Diamond homologs: Q5DRD6, Q86SJ6, Q8VHF2, Q9HBB8, Q9JIK1, Q9Y5F0, P34616, Q5DRB3, Q5DRB8, Q9Y5G6, Q9Y5H1
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
221 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 190 |
| Likely benign | 17 |
| Benign | 2 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2702 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 11:617941:T:TA | donor_gain | 1.0000 |
| 11:618119:C:CT | acceptor_gain | 1.0000 |
| 11:620062:CTCA:C | donor_loss | 1.0000 |
| 11:620163:TCCTG:T | acceptor_loss | 1.0000 |
| 11:620164:CCTG:C | acceptor_loss | 1.0000 |
| 11:620165:C:CC | acceptor_gain | 1.0000 |
| 11:620294:A:AC | donor_gain | 1.0000 |
| 11:620294:AC:A | donor_gain | 1.0000 |
| 11:620294:ACC:A | donor_gain | 1.0000 |
| 11:620294:ACCC:A | donor_gain | 1.0000 |
| 11:620295:C:CC | donor_gain | 1.0000 |
| 11:620295:CC:C | donor_gain | 1.0000 |
| 11:620295:CCC:C | donor_gain | 1.0000 |
| 11:620295:CCCC:C | donor_gain | 1.0000 |
| 11:620295:CCCCT:C | donor_gain | 1.0000 |
| 11:620367:C:CT | acceptor_gain | 1.0000 |
| 11:620369:C:CT | acceptor_gain | 1.0000 |
| 11:620390:C:CT | acceptor_gain | 1.0000 |
| 11:620391:A:T | acceptor_gain | 1.0000 |
| 11:620395:A:AC | acceptor_gain | 1.0000 |
| 11:620399:C:CT | acceptor_gain | 1.0000 |
| 11:620400:G:T | acceptor_gain | 1.0000 |
| 11:621112:A:AC | donor_gain | 1.0000 |
| 11:621113:C:CC | donor_gain | 1.0000 |
| 11:621113:CTGAG:C | donor_gain | 1.0000 |
| 11:621117:G:C | donor_gain | 1.0000 |
| 11:621133:AG:A | donor_gain | 1.0000 |
| 11:621133:AGC:A | donor_gain | 1.0000 |
| 11:621134:G:C | donor_gain | 1.0000 |
| 11:621560:A:AC | donor_gain | 1.0000 |
AlphaMissense
5411 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 11:624232:C:G | C98S | 0.998 |
| 11:624233:A:T | C98S | 0.998 |
| 11:621158:G:C | F237L | 0.997 |
| 11:621158:G:T | F237L | 0.997 |
| 11:621159:A:C | F237C | 0.997 |
| 11:621160:A:G | F237L | 0.997 |
| 11:624606:A:C | F71C | 0.997 |
| 11:624606:A:G | F71S | 0.997 |
| 11:621159:A:G | F237S | 0.996 |
| 11:621846:A:C | F124C | 0.996 |
| 11:624605:A:C | F71L | 0.996 |
| 11:624605:A:T | F71L | 0.996 |
| 11:624607:A:G | F71L | 0.996 |
| 11:621846:A:G | F124S | 0.995 |
| 11:624231:A:C | C98W | 0.995 |
| 11:624233:A:G | C98R | 0.995 |
| 11:617510:A:C | F793L | 0.994 |
| 11:617510:A:T | F793L | 0.994 |
| 11:617512:A:G | F793L | 0.994 |
| 11:619541:A:G | F409S | 0.994 |
| 11:621126:C:G | C248S | 0.994 |
| 11:621127:A:G | C248R | 0.994 |
| 11:621127:A:T | C248S | 0.994 |
| 11:624232:C:T | C98Y | 0.994 |
| 11:624585:A:G | L78P | 0.994 |
| 11:624696:T:A | E41V | 0.994 |
| 11:619799:A:C | F354C | 0.993 |
| 11:620349:G:T | A276D | 0.993 |
| 11:621208:C:G | A221P | 0.993 |
| 11:621845:G:C | F124L | 0.993 |
dbSNP variants (sampled 300 via entrez): RS1000029513 (11:624305 A>G), RS1000085475 (11:619677 C>G,T), RS1000228694 (11:619696 C>T), RS1000283316 (11:623245 G>A,T), RS1000399627 (11:623426 C>T), RS1000541351 (11:626871 A>C), RS1001644615 (11:623208 C>G), RS1001796230 (11:623030 C>T), RS1002033373 (11:622176 G>A), RS1002193325 (11:617968 A>G), RS1002273886 (11:619924 G>A), RS1002491176 (11:616980 T>A), RS1002868924 (11:616735 T>C), RS1002907586 (11:618261 G>A,C), RS1002928989 (11:618475 A>G,T)
Disease associations
OMIM: gene MIM:606839 | disease phenotypes:
GenCC curated gene-disease
Mondo (1): developmental and epileptic encephalopathy (MONDO:0100620)
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
2 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST003155_11 | Systemic lupus erythematosus | 9.000000e-10 |
| GCST009131_16 | Systemic sclerosis | 2.000000e-08 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
14 total (human), top 14 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| bisphenol A | decreases methylation, affects cotreatment | 1 |
| bleomycetin | decreases expression | 1 |
| 2-palmitoylglycerol | increases expression | 1 |
| bisphenol S | decreases methylation | 1 |
| Sunitinib | increases expression | 1 |
| Fulvestrant | affects cotreatment, decreases methylation | 1 |
| Arsenic | affects methylation | 1 |
| Benzo(a)pyrene | decreases methylation | 1 |
| Cisplatin | decreases expression | 1 |
| Tobacco Smoke Pollution | affects expression | 1 |
| Triclosan | decreases expression | 1 |
| Urethane | increases expression | 1 |
| Valproic Acid | decreases expression, increases methylation | 1 |
| Aflatoxin B1 | decreases expression | 1 |
Clinical trials (associated diseases)
22 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT03347526 | PHASE3 | SUSPENDED | A Novel Approach to Infantile Spasms |
| NCT03421496 | PHASE3 | TERMINATED | A Study to Assess Cannabidiol Oral Solution With Vigabatrin as Initial Therapy in Participants With Infantile Spasms |
| NCT06719141 | PHASE3 | RECRUITING | A Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathies (DEE) |
| NCT06908226 | PHASE3 | ENROLLING_BY_INVITATION | A Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathy (DEE) |
| NCT04289467 | PHASE2 | RECRUITING | Treatment of Refractory Infantile Spasms With Fenfluramine |
| NCT05626634 | PHASE2 | COMPLETED | Open-label, Long-term Safety Study of LP352 in Subjects With Developmental and Epileptic Encephalopathy |
| NCT04727970 | PHASE1 | COMPLETED | Tricaprilin Infantile Spasms Pilot Study |
| NCT06700811 | PHASE1 | RECRUITING | Ketogenic Diet for Prevention of Epileptic Spasms in Infantile Onset Genetic Epilepsies |
| NCT03876444 | PHASE2/PHASE3 | UNKNOWN | Intravenous Methylprednisolone Versus Oral Prednisolone for Infantile Spasms |
| NCT05279118 | PHASE2/PHASE3 | ACTIVE_NOT_RECRUITING | Ketogenic Diet vs ACTH for the Treatment of Children With West Syndrome |
| NCT05364021 | PHASE1/PHASE2 | COMPLETED | Study to Investigate LP352 in Subjects With Developmental and Epileptic Encephalopathies |
| NCT06983158 | PHASE1/PHASE2 | SUSPENDED | A Clinical Trial of CAP-002 Gene Therapy in Pediatric Patients With Syntaxin-Binding Protein 1 (STXBP1) Encephalopathy |
| NCT04937062 | EARLY_PHASE1 | ACTIVE_NOT_RECRUITING | Phenylbutyrate for Monogenetic Developmental and Epileptic Encephalopathy |
| NCT04302116 | Not specified | RECRUITING | Vigabatrin With High Dose Prednisolone Combination Therapy vs Vigabatrin Alone for Infantile Spasm |
| NCT05538936 | Not specified | COMPLETED | The Effect of Spa and Massage on Babies on Colic Symptoms |
| NCT06149663 | Not specified | AVAILABLE | Intermediate-Size Expanded Access Protocol (EAP) for LP352 |
| NCT06266234 | Not specified | RECRUITING | Characterization by Automated System on Infantile Spasmes |
| NCT06380192 | Not specified | RECRUITING | Developmental and Epileptic Encephalopathy of Genetic Etiology: Natural History Through Reuse of Clinical Data |
| NCT07396883 | Not specified | NOT_YET_RECRUITING | Developmental and Epileptic Encephalopathies Diagnosed Via Long-read Genome Sequencing |
| NCT07413211 | Not specified | RECRUITING | Genetic Developmental and Epileptic Encephalopathy Natural History Study for Clinical Trial Readiness |
| NCT07531511 | Not specified | NOT_YET_RECRUITING | SLC6A1-NDD Prospective Longitudinal Natural History Study |
| NCT07585643 | Not specified | NOT_YET_RECRUITING | IBIS - Investigating Reliability of BIS and SEDLINE Monitoring in Children With Developmental and Epileptic Encephalopathies (DEE). |
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): developmental and epileptic encephalopathy