LRRTM2
geneOn this page
Also known as KIAA0416
Summary
LRRTM2 (leucine rich repeat transmembrane neuronal 2, HGNC:19409) is a protein-coding gene on chromosome 5q31.2, encoding Leucine-rich repeat transmembrane neuronal protein 2 (O43300). Involved in the development and maintenance of excitatory synapses in the vertebrate nervous system.
Predicted to enable neurexin family protein binding activity. Predicted to be involved in regulation of postsynaptic density assembly. Predicted to act upstream of or within several processes, including long-term synaptic potentiation; negative regulation of receptor internalization; and positive regulation of synapse assembly. Is active in GABA-ergic synapse and postsynaptic specialization membrane.
Source: NCBI Gene 26045 — RefSeq curated summary.
At a glance
- GWAS associations: 2
- Clinical variants (ClinVar): 3 total — 1 pathogenic
- MANE Select transcript:
NM_015564
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:19409 |
| Approved symbol | LRRTM2 |
| Name | leucine rich repeat transmembrane neuronal 2 |
| Location | 5q31.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | KIAA0416 |
| Ensembl gene | ENSG00000146006 |
| Ensembl biotype | protein_coding |
| OMIM | 610868 |
| Entrez | 26045 |
Gene structure
Transcript identifiers
Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined
ENST00000274711, ENST00000518785, ENST00000521094, ENST00000523537
RefSeq mRNA: 1 — MANE Select: NM_015564
NM_015564
CCDS: CCDS47272
Canonical transcript exons
ENST00000274711 — 2 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000973454 | 138868921 | 138874556 |
| ENSE00002135434 | 138874908 | 138875335 |
Expression profiles
Bgee: expression breadth ubiquitous, 203 present calls, max score 96.68.
FANTOM5 (CAGE): breadth broad, TPM avg 4.1605 / max 396.7823, expressed in 222 samples.
FANTOM5 promoters (5 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 63725 | 2.0367 | 159 |
| 63724 | 1.5218 | 143 |
| 63723 | 0.2981 | 93 |
| 63726 | 0.2299 | 91 |
| 63722 | 0.0741 | 43 |
Top tissues by expression
290 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| lateral nuclear group of thalamus | UBERON:0002736 | 96.68 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 95.34 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 94.85 | gold quality |
| orbitofrontal cortex | UBERON:0004167 | 94.66 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 94.12 | gold quality |
| cortical plate | UBERON:0005343 | 93.93 | gold quality |
| parietal lobe | UBERON:0001872 | 92.75 | gold quality |
| entorhinal cortex | UBERON:0002728 | 92.72 | gold quality |
| CA1 field of hippocampus | UBERON:0003881 | 92.64 | gold quality |
| postcentral gyrus | UBERON:0002581 | 92.36 | gold quality |
| frontal pole | UBERON:0002795 | 92.23 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 91.99 | gold quality |
| pigmented layer of retina | UBERON:0001782 | 90.91 | gold quality |
| pons | UBERON:0000988 | 90.89 | gold quality |
| lateral globus pallidus | UBERON:0002476 | 90.85 | gold quality |
| occipital lobe | UBERON:0002021 | 90.16 | gold quality |
| corpus callosum | UBERON:0002336 | 90.02 | gold quality |
| primary visual cortex | UBERON:0002436 | 89.57 | gold quality |
| superior vestibular nucleus | UBERON:0007227 | 89.48 | gold quality |
| buccal mucosa cell | CL:0002336 | 89.09 | gold quality |
| ganglionic eminence | UBERON:0004023 | 88.96 | gold quality |
| dorsal plus ventral thalamus | UBERON:0001897 | 88.58 | gold quality |
| ventral tegmental area | UBERON:0002691 | 88.19 | gold quality |
| substantia nigra pars compacta | UBERON:0001965 | 87.19 | gold quality |
| Brodmann (1909) area 10 | UBERON:0013541 | 86.79 | gold quality |
| cerebellar vermis | UBERON:0004720 | 86.50 | gold quality |
| substantia nigra pars reticulata | UBERON:0001966 | 86.39 | gold quality |
| prefrontal cortex | UBERON:0000451 | 86.28 | gold quality |
| middle frontal gyrus | UBERON:0002702 | 85.81 | gold quality |
| medulla oblongata | UBERON:0001896 | 85.41 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 4.20 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
233 targeting LRRTM2, 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-6867-5P | 100.00 | 82.21 | 3464 |
| HSA-MIR-4533 | 100.00 | 69.48 | 2758 |
| HSA-MIR-3064-3P | 100.00 | 70.09 | 1254 |
| HSA-MIR-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-1277-5P | 100.00 | 73.95 | 5056 |
| HSA-MIR-5692B | 100.00 | 71.32 | 2622 |
| HSA-MIR-5692C | 100.00 | 71.32 | 2622 |
| HSA-MIR-30A-5P | 100.00 | 76.31 | 3233 |
| HSA-MIR-30B-5P | 100.00 | 76.29 | 3248 |
| HSA-MIR-30C-5P | 100.00 | 76.29 | 3248 |
| HSA-MIR-30D-5P | 100.00 | 76.32 | 3233 |
| HSA-MIR-30E-5P | 100.00 | 76.32 | 3242 |
| HSA-MIR-4668-3P | 100.00 | 68.74 | 2635 |
| HSA-MIR-656-3P | 100.00 | 72.15 | 2788 |
| HSA-MIR-3646 | 100.00 | 73.56 | 5283 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-4534 | 99.99 | 66.58 | 1907 |
| HSA-MIR-34A-5P | 99.99 | 71.21 | 1784 |
| HSA-MIR-449A | 99.99 | 71.05 | 1776 |
| HSA-MIR-3662 | 99.99 | 73.82 | 5684 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-5696 | 99.98 | 72.36 | 4487 |
| HSA-MIR-433-3P | 99.98 | 69.37 | 1203 |
| HSA-MIR-19A-3P | 99.98 | 75.33 | 2762 |
| HSA-MIR-19B-3P | 99.98 | 75.44 | 2754 |
| HSA-MIR-4775 | 99.98 | 75.00 | 6394 |
| HSA-MIR-568 | 99.98 | 69.86 | 2084 |
| HSA-MIR-3148 | 99.97 | 75.06 | 6478 |
| HSA-MIR-302C-5P | 99.97 | 72.56 | 3642 |
| HSA-MIR-34C-5P | 99.97 | 70.45 | 1577 |
Literature-anchored findings (GeneRIF, showing 2)
- CTNNA1 and CTNNA2 contain alternative 5’ exons linked to bidirectional promoters that are shared with the antisense oriented LRRTM2 and LRRTM1 genes, respectively. (PMID:21708131)
- The Nrxn1beta-LRRTM2 interface involves Ca(2+)-mediated interactions and overlaps with the Nrxn-neuroligin interface. (PMID:30262834)
Cross-species orthologs
7 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | lrrtm2 | ENSDARG00000071374 |
| mus_musculus | Lrrtm2 | ENSMUSG00000071862 |
| rattus_norvegicus | Lrrtm2 | ENSRNOG00000047085 |
| drosophila_melanogaster | Con | FBGN0005775 |
| drosophila_melanogaster | kek3 | FBGN0028370 |
| caenorhabditis_elegans | lron-9 | WBGENE00011971 |
| caenorhabditis_elegans | WBGENE00020649 |
Paralogs (22): CHADL (ENSG00000100399), LGI1 (ENSG00000108231), LGR6 (ENSG00000133067), CHAD (ENSG00000136457), LRIG3 (ENSG00000139263), LGR5 (ENSG00000139292), LRIG1 (ENSG00000144749), LRIT1 (ENSG00000148602), LGI2 (ENSG00000153012), LGI4 (ENSG00000153902), LRRC52 (ENSG00000162763), ELFN2 (ENSG00000166897), LGI3 (ENSG00000168481), LRG1 (ENSG00000171236), CPN2 (ENSG00000178772), LRIT3 (ENSG00000183423), LRRC26 (ENSG00000184709), LRIG2 (ENSG00000198799), LGR4 (ENSG00000205213), ELFN1 (ENSG00000225968), LRRC24 (ENSG00000254402), TRIL (ENSG00000255690)
Protein
Protein identifiers
Leucine-rich repeat transmembrane neuronal protein 2 — O43300 (reviewed: O43300)
Alternative names: Leucine-rich repeat neuronal 2 protein
All UniProt accessions (3): E5RHE5, E5RIQ2, O43300
UniProt curated annotations — full annotation on UniProt →
Function. Involved in the development and maintenance of excitatory synapses in the vertebrate nervous system. Regulates surface expression of AMPA receptors and instructs the development of functional glutamate release sites. Acts as a ligand for the presynaptic receptors NRXN1-A and NRXN1-B.
Subunit / interactions. Interacts with DLG4. Interacts with neurexin NRXN1; interaction is mediated by heparan sulfate glycan modification on neurexin.
Subcellular location. Cell membrane. Postsynaptic cell membrane.
Tissue specificity. Expressed in neuronal tissues.
Domain organisation. Synaptogenic effects are mediated by the extracellular LRR region.
Similarity. Belongs to the LRRTM family.
RefSeq proteins (1): NP_056379* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR001611 | Leu-rich_rpt | Repeat |
| IPR003591 | Leu-rich_rpt_typical-subtyp | Repeat |
| IPR032675 | LRR_dom_sf | Homologous_superfamily |
| IPR050467 | LRFN | Family |
Pfam: PF13855
UniProt features (51 total): strand 15, repeat 10, turn 8, helix 5, glycosylation site 4, domain 2, topological domain 2, signal peptide 1, chain 1, short sequence motif 1, sequence conflict 1, transmembrane region 1
Structure
Experimental structures (PDB)
2 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 5Z8X | X-RAY DIFFRACTION | 3.15 |
| 5Z8Y | X-RAY DIFFRACTION | 3.4 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-O43300-F1 | 79.50 | 0.61 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Glycosylation sites (4): 57, 126, 243, 362
Function
Pathways and Gene Ontology
Reactome pathways
3 pathways
| ID | Pathway |
|---|---|
| R-HSA-6794361 | Neurexins and neuroligins |
| R-HSA-112316 | Neuronal System |
| R-HSA-6794362 | Protein-protein interactions at synapses |
MSigDB gene sets: 205 (showing top):
GOBP_SYNAPSE_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_SYNAPSE_ASSEMBLY, GOBP_NEGATIVE_REGULATION_OF_ENDOCYTOSIS, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP, GOBP_CELL_CELL_SIGNALING, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, MORF_ZNF10, GOBP_NEGATIVE_REGULATION_OF_TRANSPORT
GO Biological Process (5): negative regulation of receptor internalization (GO:0002091), synapse organization (GO:0050808), positive regulation of synapse assembly (GO:0051965), long-term synaptic potentiation (GO:0060291), regulation of postsynaptic density assembly (GO:0099151)
GO Molecular Function (2): neurexin family protein binding (GO:0042043), protein binding (GO:0005515)
GO Cellular Component (12): obsolete extracellular space (GO:0005615), excitatory synapse (GO:0060076), Schaffer collateral - CA1 synapse (GO:0098685), hippocampal mossy fiber to CA3 synapse (GO:0098686), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), GABA-ergic synapse (GO:0098982), postsynaptic specialization membrane (GO:0099634), plasma membrane (GO:0005886), membrane (GO:0016020), synapse (GO:0045202), postsynaptic membrane (GO:0045211)
Reactome top-level categories
Rollup of top-2 pathways:
| Category | Pathways |
|---|---|
| Protein-protein interactions at synapses | 1 |
| Neuronal System | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| synapse | 4 |
| postsynaptic membrane | 2 |
| synaptic membrane | 2 |
| regulation of receptor internalization | 1 |
| receptor internalization | 1 |
| negative regulation of receptor-mediated endocytosis | 1 |
| cell junction organization | 1 |
| synapse assembly | 1 |
| positive regulation of nervous system development | 1 |
| regulation of synapse assembly | 1 |
| positive regulation of cell junction assembly | 1 |
| regulation of synaptic plasticity | 1 |
| positive regulation of synaptic transmission | 1 |
| postsynaptic density assembly | 1 |
| regulation of postsynaptic specialization assembly | 1 |
| regulation of excitatory synapse assembly | 1 |
| regulation of postsynaptic density organization | 1 |
| signaling receptor binding | 1 |
| binding | 1 |
| thorny excrescence | 1 |
| neuron to neuron synapse | 1 |
| hippocampal mossy fiber expansion | 1 |
| postsynaptic density | 1 |
| postsynaptic specialization membrane | 1 |
| postsynaptic specialization | 1 |
| membrane | 1 |
| cell periphery | 1 |
| cellular anatomical structure | 1 |
| cell junction | 1 |
| postsynapse | 1 |
Protein interactions and networks
STRING
1400 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| LRRTM2 | NRXN1 | Q9ULB1 | 992 |
| LRRTM2 | NRXN2 | Q9P2S2 | 977 |
| LRRTM2 | CEMIP2 | Q9UHN6 | 924 |
| LRRTM2 | DLG4 | P78352 | 891 |
| LRRTM2 | NLGN1 | Q8N2Q7 | 806 |
| LRRTM2 | NXN | Q6DKJ4 | 801 |
| LRRTM2 | CTNNA1 | P35221 | 730 |
| LRRTM2 | NLGN4X | Q8N0W4 | 717 |
| LRRTM2 | NRXN3 | Q9Y4C0 | 714 |
| LRRTM2 | NLGN3 | Q9NZ94 | 712 |
| LRRTM2 | CBLN1 | P02682 | 688 |
| LRRTM2 | NLGN2 | Q8NFZ4 | 649 |
| LRRTM2 | GRIA2 | P42262 | 572 |
| LRRTM2 | GPC4 | O75487 | 529 |
| LRRTM2 | CADM1 | Q9BY67 | 527 |
IntAct
28 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| NRXN1 | LRRTM2 | psi-mi:“MI:0407”(direct interaction) | 0.690 |
| NRXN1 | LRRTM2 | psi-mi:“MI:0915”(physical association) | 0.690 |
| LRRTM2 | NRXN1 | psi-mi:“MI:0915”(physical association) | 0.690 |
| LRRTM2 | NRXN1 | psi-mi:“MI:0407”(direct interaction) | 0.690 |
| TNF | LRRTM2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| TMEM120B | LRRTM2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| LRRTM2 | TNF | psi-mi:“MI:0915”(physical association) | 0.560 |
| LRRTM2 | GPC3 | psi-mi:“MI:0914”(association) | 0.530 |
| LRRTM2 | NRXN1 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| LRRTM2 | FGFR4 | psi-mi:“MI:0915”(physical association) | 0.400 |
| LRRTM2 | IGDCC4 | psi-mi:“MI:0915”(physical association) | 0.400 |
| LRRTM2 | MICA | psi-mi:“MI:0915”(physical association) | 0.400 |
| LRRTM2 | NRG2 | psi-mi:“MI:0915”(physical association) | 0.400 |
| LRRTM2 | OSCAR | psi-mi:“MI:0915”(physical association) | 0.400 |
| LRRTM2 | PRTG | psi-mi:“MI:0915”(physical association) | 0.400 |
| LRRTM2 | SEMA4G | psi-mi:“MI:0915”(physical association) | 0.400 |
| LRRTM2 | TREML2 | psi-mi:“MI:0915”(physical association) | 0.400 |
| LRRTM2 | UNC5A | psi-mi:“MI:0915”(physical association) | 0.400 |
| Mecom | ESYT2 | psi-mi:“MI:0914”(association) | 0.350 |
| LRRTM2 | PTPRD | psi-mi:“MI:0914”(association) | 0.350 |
| DCAF4 | IGLL5 | psi-mi:“MI:0914”(association) | 0.350 |
| TTI2 | LRRTM2 | psi-mi:“MI:0914”(association) | 0.350 |
| TMEM120B | LRRTM2 | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (29): ACTA2 (Affinity Capture-MS), DAD1 (Affinity Capture-MS), CNPY3 (Affinity Capture-MS), TYW1 (Affinity Capture-MS), TOMM40 (Affinity Capture-MS), TMEM38B (Affinity Capture-MS), GPC3 (Affinity Capture-MS), CNPY4 (Affinity Capture-MS), PDE3B (Affinity Capture-MS), PTPRD (Affinity Capture-MS), ST7 (Affinity Capture-MS), TMEM38B (Affinity Capture-MS), CNPY3 (Affinity Capture-MS), CNPY4 (Affinity Capture-MS), GPC3 (Affinity Capture-MS)
ESM2 similar proteins: A0N0X6, A4IIW9, B0BLW3, B1H134, B1H234, B4F7C5, D3ZAL8, D3ZTV3, D4A7P2, E5DHB5, F1NUK7, F7D3V9, O43155, O43300, O94898, P58681, Q32Q07, Q3SXY7, Q3URE9, Q504C1, Q50L44, Q52KR2, Q5R482, Q5R6T0, Q5RDJ4, Q61809, Q66HV9, Q6RKD8, Q6UXK5, Q70AK3, Q7L985, Q80XG9, Q80ZD7, Q80ZD8, Q80ZD9, Q86VH4, Q86VH5, Q8BGA3, Q8BGT1, Q8BLU0
Diamond homologs: A1A4H9, B4F7C5, D3ZAL8, D4A6D8, D4A7P2, O43300, O75093, P58874, Q5R6B1, Q80XG9, Q86UE6, Q86VH4, Q86VH5, Q8BGA3, Q8BZ81, Q8C2S7, Q8K377, Q920A0, Q9BGP6, Q9UBM4, O02678, Q3ZBN5, Q99MQ4, Q9BXN1, Q80ZD7, Q80ZD8
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
3 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 1 |
| Likely benign | 0 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 3381259 | NC_000005.9:g.(?138117614)(138269778_?)del | Pathogenic |
SpliceAI
340 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 5:138873017:T:TA | donor_gain | 0.9800 |
| 5:138873017:TC:T | donor_gain | 0.9800 |
| 5:138873015:CT:C | donor_gain | 0.9700 |
| 5:138873016:TT:T | donor_gain | 0.9700 |
| 5:138872979:A:AC | donor_gain | 0.9600 |
| 5:138872980:T:C | donor_gain | 0.9600 |
| 5:138872979:AT:A | donor_gain | 0.9500 |
| 5:138874906:A:AC | donor_gain | 0.9400 |
| 5:138874907:C:CC | donor_gain | 0.9400 |
| 5:138874906:AC:A | donor_gain | 0.9300 |
| 5:138874907:CC:C | donor_gain | 0.9300 |
| 5:138873020:CATT:C | donor_gain | 0.9200 |
| 5:138869172:T:C | acceptor_gain | 0.9000 |
| 5:138874902:ACTT:A | donor_loss | 0.9000 |
| 5:138874903:CTT:C | donor_loss | 0.9000 |
| 5:138874904:TTACC:T | donor_loss | 0.9000 |
| 5:138874905:TAC:T | donor_loss | 0.9000 |
| 5:138874907:C:T | donor_loss | 0.9000 |
| 5:138875164:C:CT | donor_gain | 0.9000 |
| 5:138875181:G:C | donor_gain | 0.9000 |
| 5:138875237:A:C | donor_gain | 0.9000 |
| 5:138871239:T:TA | donor_gain | 0.8600 |
| 5:138871240:A:AA | donor_gain | 0.8600 |
| 5:138875165:C:CT | donor_gain | 0.8600 |
| 5:138874906:ACC:A | donor_gain | 0.8200 |
| 5:138874907:CCC:C | donor_gain | 0.8200 |
| 5:138875163:TC:T | donor_gain | 0.8100 |
| 5:138872975:A:AC | donor_gain | 0.8000 |
| 5:138872976:C:CC | donor_gain | 0.8000 |
| 5:138873294:CCCG:C | donor_gain | 0.7900 |
AlphaMissense
3396 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 5:138873544:G:C | C339W | 1.000 |
| 5:138873545:C:G | C339S | 1.000 |
| 5:138873546:A:G | C339R | 1.000 |
| 5:138873546:A:T | C339S | 1.000 |
| 5:138873622:C:A | W313C | 1.000 |
| 5:138873622:C:G | W313C | 1.000 |
| 5:138873624:A:G | W313R | 1.000 |
| 5:138873624:A:T | W313R | 1.000 |
| 5:138873932:A:G | L210P | 1.000 |
| 5:138873545:C:T | C339Y | 0.999 |
| 5:138873616:G:C | C315W | 0.999 |
| 5:138873617:C:G | C315S | 0.999 |
| 5:138873617:C:T | C315Y | 0.999 |
| 5:138873618:A:G | C315R | 0.999 |
| 5:138873618:A:T | C315S | 0.999 |
| 5:138873628:A:C | N311K | 0.999 |
| 5:138873628:A:T | N311K | 0.999 |
| 5:138873700:G:C | N287K | 0.999 |
| 5:138873700:G:T | N287K | 0.999 |
| 5:138873716:A:G | L282P | 0.999 |
| 5:138873772:A:C | N263K | 0.999 |
| 5:138873772:A:T | N263K | 0.999 |
| 5:138873782:A:G | L260P | 0.999 |
| 5:138873788:A:G | L258P | 0.999 |
| 5:138873844:G:C | N239K | 0.999 |
| 5:138873844:G:T | N239K | 0.999 |
| 5:138873845:T:A | N239I | 0.999 |
| 5:138873846:T:A | N239Y | 0.999 |
| 5:138873860:A:G | L234P | 0.999 |
| 5:138873916:G:C | N215K | 0.999 |
dbSNP variants (sampled 300 via entrez): RS1000132696 (5:138870732 A>G), RS1000140136 (5:138873394 A>G), RS1000185378 (5:138871019 G>A,C), RS1001103460 (5:138875460 C>G,T), RS1001554822 (5:138875250 A>G), RS1001930834 (5:138877066 T>G), RS1001931905 (5:138875186 T>C), RS1002088357 (5:138869794 CTT>C), RS1002384349 (5:138874805 A>G), RS1002595650 (5:138871762 G>A,C), RS1003557961 (5:138868494 A>G), RS1003597731 (5:138873267 A>G), RS1003654921 (5:138872794 A>G), RS1004007723 (5:138870375 T>C), RS1004123514 (5:138870654 A>G)
Disease associations
OMIM: gene MIM:610868 | disease phenotypes:
GenCC curated gene-disease
Mondo (1): hereditary neoplastic syndrome (MONDO:0015356)
Orphanet (1): Inherited cancer-predisposing syndrome (Orphanet:140162)
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
2 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST010725_68 | Malaria | 4.000000e-07 |
| GCST010725_7 | Malaria | 2.000000e-06 |
MeSH disease descriptors (1)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D009386 | Neoplastic Syndromes, Hereditary | C04.700; C16.320.700 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
10 total (human), top 10 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Cadmium Chloride | decreases expression, increases abundance, increases expression | 2 |
| sodium arsenite | affects expression | 1 |
| bisphenol S | decreases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| Cadmium | decreases expression, increases abundance | 1 |
| Cisplatin | increases expression | 1 |
| Lead | affects expression | 1 |
| Tretinoin | increases expression | 1 |
| 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide | increases expression | 1 |
| Lactic Acid | increases expression | 1 |
Clinical trials (associated diseases)
29 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT00001496 | Not specified | COMPLETED | Establishment of Normal Breast Epithelial Cell Lines From Patients at High Risk for Breast Cancer |
| NCT00001898 | Not specified | COMPLETED | Microarray Analysis for Human Genetic Disease |
| NCT00026884 | Not specified | RECRUITING | Collection of Serum and Tissue Samples From Patients With Biopsy-Proved or Suspected Malignant Disease |
| NCT02289326 | Not specified | COMPLETED | Biomarker Monitoring in TP53 Mutation Carriers |
| NCT02958462 | Not specified | RECRUITING | Pre-myeloid Cancer and Bone Marrow Failure Clinic Study |
| NCT03160274 | Not specified | RECRUITING | Genetic Analysis of Pheochromocytomas, Paragangliomas and Associated Conditions |
| NCT03426878 | Not specified | COMPLETED | Cancer Health Assessments Reaching Many |
| NCT03857594 | Not specified | ACTIVE_NOT_RECRUITING | Integrative Sequencing In Germline and Hereditary Tumours |
| NCT03973450 | Not specified | UNKNOWN | Epidemiology of Pituitary Tumours: Prevalence of Associated Neoplasia |
| NCT03979612 | Not specified | UNKNOWN | Evaluation of the Adhesion to the GENEPY Network |
| NCT04261972 | Not specified | ACTIVE_NOT_RECRUITING | Cell-free DNA in Hereditary And High-Risk Malignancies 1 |
| NCT04494945 | Not specified | RECRUITING | Identifying and Caring for Individuals With Inherited Cancer Syndrome |
| NCT04541654 | Not specified | RECRUITING | Li-Fraumeni & TP53 (LiFT UP): Understanding and Progress |
| NCT04763915 | Not specified | ACTIVE_NOT_RECRUITING | Improving Care After Inherited Cancer Testing |
| NCT05562778 | Not specified | RECRUITING | Chatbot to Maximize Hereditary Cancer Genetic Risk Assessment |
| NCT05664867 | Not specified | RECRUITING | Implementation of Population Cancer Genetic Services in Federally Qualified Health Centers (FQHC) |
| NCT05721326 | Not specified | COMPLETED | Sequential EHR Based Interventions to Increase Genetic Testing for Breast and Ovarian Cancer Predisposition |
| NCT06096688 | Not specified | RECRUITING | Discovering New Targets for Colorectal and Endometrial Cancer Risk Reduction |
| NCT06654466 | Not specified | RECRUITING | Closing the GAPS: Guideline Adherence, Prevention and Surveillance in Hereditary Cancer |
| NCT06708429 | Not specified | RECRUITING | Lynch Syndrome X-Talk of Enteral Mucosa With Immune System |
| NCT06726642 | Not specified | RECRUITING | CfDNA in Hereditary And High-risk Malignancies 2 |
| NCT06914726 | Not specified | ENROLLING_BY_INVITATION | Patient Centered Clinical Decision Support for Hereditary Cancer Syndromes |
| NCT06927947 | Not specified | RECRUITING | Navigation Interventions to Improve Cascade Genetic Testing Among Relatives of Patients With Hereditary Cancer Syndromes |
| NCT06999954 | Not specified | RECRUITING | Shwachman-Diamond Syndrome Global Patient Survey and Partnering Platform |
| NCT07052266 | Not specified | RECRUITING | Trial of Combined Obstetric Carrier Screening and Hereditary Cancer Screening |
| NCT07195071 | Not specified | RECRUITING | Feasibility Trial of Combination of Obstetrical Carrier Screening and Hereditary Cancer Screening |
| NCT07378423 | Not specified | RECRUITING | Questionnaire on Congenital Cancer Signs Through Self-Assessment |
| NCT07381985 | Not specified | ENROLLING_BY_INVITATION | Strategy for Management of Patients With Hereditary Cancer Syndromes (HCS) in a Rural Environment |
| NCT07542405 | Not specified | NOT_YET_RECRUITING | A Web-Based Program (Kindred) to Improve the Understanding of Genetic Cancer Risk and Cancer Genetic Testing in African American Families |
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): hereditary neoplastic syndrome