LILRA2
gene geneOn this page
Also known as LIR-7ILT1CD85hLIR7
Summary
LILRA2 (leukocyte immunoglobulin like receptor A2, HGNC:6603) is a protein-coding gene on chromosome 19q13.42, encoding Leukocyte immunoglobulin-like receptor subfamily A member 2 (Q8N149). Part of the innate immune responses against microbial infection.
This gene encodes a member of a family of immunoreceptors that are expressed predominantly on monocytes and B cells, and at lower levels on dendritic cells and natural killer cells. The encoded protein is an activating receptor that inhibits dendritic cell differentiation and antigen presentation and suppresses innate immune response. Alternatively spliced transcript variants encoding different isoforms have been found. This gene is located in a cluster of related genes on chromosome 19 and there is a pseudogene for this gene on chromosome 3.
Source: NCBI Gene 11027 — RefSeq curated summary.
At a glance
- Clinical variants (ClinVar): 141 total
- MANE Select transcript:
NM_001130917
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:6603 |
| Approved symbol | LILRA2 |
| Name | leukocyte immunoglobulin like receptor A2 |
| Location | 19q13.42 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | LIR-7, ILT1, CD85h, LIR7 |
| Ensembl gene | ENSG00000239998 |
| Ensembl biotype | protein_coding |
| OMIM | 604812 |
| Entrez | 11027 |
Gene structure
Transcript identifiers
Ensembl transcripts: 13 — 12 protein_coding, 1 protein_coding_CDS_not_defined
ENST00000251376, ENST00000251377, ENST00000391737, ENST00000391738, ENST00000439534, ENST00000472992, ENST00000495786, ENST00000889282, ENST00000889283, ENST00000889284, ENST00000889285, ENST00000954510, ENST00000954511
RefSeq mRNA: 4 — MANE Select: NM_001130917
NM_001130917, NM_001290270, NM_001290271, NM_006866
CCDS: CCDS12900, CCDS46179, CCDS74453
Canonical transcript exons
ENST00000391738 — 8 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001373400 | 54573790 | 54573912 |
| ENSE00003459519 | 54574301 | 54574582 |
| ENSE00003624947 | 54574076 | 54574111 |
| ENSE00003888857 | 54575256 | 54575552 |
| ENSE00003891467 | 54587201 | 54590287 |
| ENSE00003894905 | 54575807 | 54576109 |
| ENSE00003895250 | 54587010 | 54587060 |
| ENSE00003895381 | 54574731 | 54575033 |
Expression profiles
Bgee: expression breadth ubiquitous, 130 present calls, max score 98.24.
FANTOM5 (CAGE): breadth broad, TPM avg 7.0833 / max 359.1754, expressed in 371 samples.
FANTOM5 promoters (4 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 177531 | 5.7953 | 337 |
| 177529 | 0.7926 | 183 |
| 177530 | 0.4129 | 174 |
| 177528 | 0.0825 | 48 |
Top tissues by expression
134 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| blood | UBERON:0000178 | 98.24 | gold quality |
| granulocyte | CL:0000094 | 98.17 | gold quality |
| leukocyte | CL:0000738 | 97.80 | gold quality |
| monocyte | CL:0000576 | 97.73 | gold quality |
| spleen | UBERON:0002106 | 93.09 | gold quality |
| bone marrow | UBERON:0002371 | 92.99 | gold quality |
| bone marrow cell | CL:0002092 | 90.48 | gold quality |
| vermiform appendix | UBERON:0001154 | 86.60 | gold quality |
| right lung | UBERON:0002167 | 81.44 | gold quality |
| upper lobe of left lung | UBERON:0008952 | 79.13 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 74.57 | gold quality |
| lung | UBERON:0002048 | 74.45 | gold quality |
| right adrenal gland cortex | UBERON:0035827 | 73.93 | gold quality |
| smooth muscle tissue | UBERON:0001135 | 73.27 | gold quality |
| gall bladder | UBERON:0002110 | 72.72 | gold quality |
| omental fat pad | UBERON:0010414 | 71.89 | gold quality |
| right adrenal gland | UBERON:0001233 | 71.66 | gold quality |
| substantia nigra | UBERON:0002038 | 71.51 | gold quality |
| placenta | UBERON:0001987 | 71.50 | gold quality |
| adipose tissue | UBERON:0001013 | 71.05 | gold quality |
| right coronary artery | UBERON:0001625 | 70.99 | gold quality |
| left adrenal gland | UBERON:0001234 | 70.95 | gold quality |
| subcutaneous adipose tissue | UBERON:0002190 | 70.40 | gold quality |
| left adrenal gland cortex | UBERON:0035825 | 70.37 | gold quality |
| left uterine tube | UBERON:0001303 | 70.20 | gold quality |
| descending thoracic aorta | UBERON:0002345 | 69.32 | gold quality |
| left coronary artery | UBERON:0001626 | 69.13 | gold quality |
| lymph node | UBERON:0000029 | 68.81 | gold quality |
| adrenal gland | UBERON:0002369 | 68.29 | gold quality |
| liver | UBERON:0002107 | 67.82 | gold quality |
Single-cell (SCXA)
Detected in 5 experiment(s), a significant marker in 5.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-CURD-46 | yes | 32.52 |
| E-CURD-88 | yes | 21.13 |
| E-MTAB-6701 | yes | 13.13 |
| E-HCAD-10 | yes | 7.76 |
| E-ANND-3 | yes | 4.53 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
12 targeting LILRA2, 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-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-372-5P | 99.41 | 69.11 | 2299 |
| HSA-MIR-488-5P | 99.28 | 68.12 | 821 |
| HSA-MIR-10524-5P | 99.05 | 66.08 | 963 |
| HSA-MIR-140-3P | 99.04 | 67.69 | 1324 |
| HSA-MIR-6876-3P | 98.97 | 65.69 | 765 |
| HSA-MIR-455-3P | 98.94 | 67.68 | 878 |
| HSA-MIR-626 | 98.89 | 66.21 | 762 |
| HSA-MIR-198 | 98.70 | 67.32 | 920 |
| HSA-MIR-338-3P | 98.14 | 67.38 | 1137 |
| HSA-MIR-6802-3P | 97.29 | 65.42 | 613 |
| HSA-MIR-517-5P | 97.13 | 68.43 | 781 |
Literature-anchored findings (GeneRIF, showing 11)
- LIR7 is an activating receptor for eosinophils that elicited the release of cytotoxic granule proteins, de novo lipid mediator generation, and cytokine release through vesicular transport (PMID:12529506)
- Cross-linking of basophil LIR7 resulted in the concentration-dependent net release of histamine and cysteinyl leukotrienes that were maximal at 30 minutes, and of IL-4 that was maximal at 4 hours (PMID:15242876)
- Progenitor mast cells expressed cell surface activating LILRA2. Mature cord-blood-derived mast cells had detectable mRNA encoding multiple LILRs, none were expressed on the cell surface. (PMID:17998301)
- LILRA2 activation, by altering GM-CSF-induced monocyte differentiation into immature DC, provides a mechanism for down-regulating the ability of the innate immune system to activate the adaptive T cell response while promoting an inflammatory response. (PMID:18056355)
- LILRA2 Delta 419-421 isoform encoded by the splice site SNP may play a role in systemic lupus erythematosus and microscopic polyangiitis. (PMID:18273033)
- The authors report the LILRA2 extracellular D1D2 domain crystal structure, which reveals structural shifts of the corresponding MHC-binding amino acid residues in comparison with LILR B1/B2, explaining its non-binding to MHC molecules. (PMID:19230061)
- LILRA2-mediated activation of monocytes is significantly different to LPS and that LILRA2 selectively modulates LPS-mediated monocyte activation and FcgammaRI-dependent phagocytosis. (PMID:22479404)
- LILRA2 recognizes microbially cleaved antibodies and activates innate immunity, suggesting that LILRA2 detects dangerous immunological situations in which antibodies are destroyed by pathogens. (PMID:27572839)
- findings demonstrate that LILRA2 is a type of innate immune receptor in the host immune system that detects immunoglobulin abnormalities caused by microbial pathogens. (PMID:27572839)
- Molecular mechanism of the recognition of bacterially cleaved immunoglobulin by the immune regulatory receptor LILRA2. (PMID:32424043)
- Overexpression of LILRA2 indicated poor prognosis of ovarian carcinoma: A new potential biomarker and therapeutic target. (PMID:36720556)
Cross-species orthologs
15 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Lilra6 | ENSMUSG00000030427 |
| mus_musculus | Pirb | ENSMUSG00000058818 |
| mus_musculus | Lilra5 | ENSMUSG00000070873 |
| mus_musculus | Pira12 | ENSMUSG00000074417 |
| mus_musculus | Pira13 | ENSMUSG00000074419 |
| mus_musculus | Pira1 | ENSMUSG00000081665 |
| mus_musculus | Pira2 | ENSMUSG00000089942 |
| rattus_norvegicus | Lilra5 | ENSRNOG00000027808 |
| rattus_norvegicus | Lilrb3 | ENSRNOG00000046683 |
| rattus_norvegicus | Lilrb2 | ENSRNOG00000054954 |
| rattus_norvegicus | Lilrc2 | ENSRNOG00000058087 |
| rattus_norvegicus | Pirb | ENSRNOG00000058422 |
| rattus_norvegicus | LOC134485274 | ENSRNOG00000062907 |
| rattus_norvegicus | ENSRNOG00000067708 | |
| rattus_norvegicus | ENSRNOG00000069029 |
Paralogs (25): GP6 (ENSG00000088053), LILRB1 (ENSG00000104972), LILRA1 (ENSG00000104974), LILRB5 (ENSG00000105609), A1BG (ENSG00000121410), KIR2DL1 (ENSG00000125498), LILRB2 (ENSG00000131042), IGSF1 (ENSG00000147255), LAIR2 (ENSG00000167618), KIR3DL1 (ENSG00000167633), OSCAR (ENSG00000170909), FCAR (ENSG00000186431), LILRB4 (ENSG00000186818), LILRA5 (ENSG00000187116), KIR2DL4 (ENSG00000189013), VSTM1 (ENSG00000189068), NCR1 (ENSG00000189430), LILRB3 (ENSG00000204577), KIR2DS4 (ENSG00000221957), LILRA4 (ENSG00000239961), KIR3DL2 (ENSG00000240403), KIR3DL3 (ENSG00000242019), KIR2DL3 (ENSG00000243772), LILRA6 (ENSG00000244482), TARM1 (ENSG00000248385)
Protein
Protein identifiers
Leukocyte immunoglobulin-like receptor subfamily A member 2 — Q8N149 (reviewed: Q8N149)
Alternative names: CD85 antigen-like family member H, Immunoglobulin-like transcript 1, Leukocyte immunoglobulin-like receptor 7
All UniProt accessions (4): Q8N149, A0A087WT41, A8MZH0, E9PDF4
UniProt curated annotations — full annotation on UniProt →
Function. Part of the innate immune responses against microbial infection. Specifically recognizes a set of N-terminally truncated immunoglobulins that are produced via cleavage by proteases from a range of pathogenic bacteria and fungi, including L.pneumophila, M.hyorhinis, S.pneumoniae, S.aureus and C.albicans. Recognizes epitopes that are in part in the variable region of the immunoglobulin light chains, but requires also the constant region for signaling. Binds to a subset of cleaved IgM, IgG3 and IgG4 molecules, but does not bind cleaved IgA1. Binding of N-terminally truncated immunoglobulins mediates activation of neutrophils. In monocytes, activation leads to the release of CSF2, CF3, IL6, CXCL8 and CCL3 and down-regulates responses to bacterial lipopolysaccharide (LPS), possibly via down-regulation of TLR4 expression and reduced signaling via TLR4. In eosinophils, activation by ligand binding leads to the release of RNASE2, IL4 and leukotriene C4. Does not bind class I MHC antigens.
Subunit / interactions. Homodimer.
Subcellular location. Cell membrane Secreted.
Tissue specificity. Detected on the surface of all peripheral blood monocytes, neutrophils, basophils and eosinophils (at protein level). Expression levels are very low or not detectable on monocytes, T-cells, B-cells, dendritic cells and natural killer (NK) cells.
Isoforms (4)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q8N149-1 | 1 | yes |
| Q8N149-2 | 2 | |
| Q8N149-3 | 3 | |
| Q8N149-4 | 4 |
RefSeq proteins (4): NP_001124389, NP_001277199, NP_001277200, NP_006857 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR003598 | Ig_sub2 | Domain |
| IPR003599 | Ig_sub | Domain |
| IPR007110 | Ig-like_dom | Domain |
| IPR013151 | Immunoglobulin_dom | Domain |
| IPR013783 | Ig-like_fold | Homologous_superfamily |
| IPR016332 | A1B_glyco/leuk_Ig-like_rcpt | Family |
| IPR036179 | Ig-like_dom_sf | Homologous_superfamily |
| IPR050412 | Ig-like_Receptors_ImmuneReg | Family |
Pfam: PF00047, PF13895
UniProt features (44 total): strand 15, glycosylation site 7, sequence variant 5, disulfide bond 4, domain 4, splice variant 3, topological domain 2, signal peptide 1, chain 1, transmembrane region 1, modified residue 1
Structure
Experimental structures (PDB)
1 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 2OTP | X-RAY DIFFRACTION | 2.6 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q8N149-F1 | 86.47 | 0.69 |
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 (1): 404
Disulfide bonds (4): 49–97, 143–195, 244–295, 344–395
Glycosylation sites (7): 64, 103, 138, 279, 300, 339, 429
Function
Pathways and Gene Ontology
Reactome pathways
3 pathways
| ID | Pathway |
|---|---|
| R-HSA-198933 | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell |
| R-HSA-1280218 | Adaptive Immune System |
| R-HSA-168256 | Immune System |
MSigDB gene sets: 219 (showing top):
GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GOBP_POSITIVE_REGULATION_OF_CALCIUM_ION_TRANSPORT, GOBP_REGULATION_OF_CELL_ACTIVATION, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOBP_POSITIVE_REGULATION_OF_INTERLEUKIN_8_PRODUCTION, GOBP_RESPONSE_TO_PEPTIDE, GOBP_CELLULAR_RESPONSE_TO_LIPID, GOBP_CELLULAR_RESPONSE_TO_BIOTIC_STIMULUS, MODULE_45, MODULE_64, GOBP_REGULATION_OF_TOLL_LIKE_RECEPTOR_4_SIGNALING_PATHWAY, THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION, MODULE_16, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND
GO Biological Process (19): innate immune response activating cell surface receptor signaling pathway (GO:0002220), neutrophil activation involved in immune response (GO:0002283), immune response-regulating signaling pathway (GO:0002764), defense response (GO:0006952), signal transduction (GO:0007165), negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665), positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725), positive regulation of interleukin-1 beta production (GO:0032731), positive regulation of interleukin-6 production (GO:0032755), positive regulation of interleukin-8 production (GO:0032757), positive regulation of tumor necrosis factor production (GO:0032760), negative regulation of toll-like receptor 4 signaling pathway (GO:0034144), innate immune response (GO:0045087), positive regulation of cell activation (GO:0050867), positive regulation of calcium ion transport (GO:0051928), positive regulation of granulocyte colony-stimulating factor production (GO:0071657), interleukin-10-mediated signaling pathway (GO:0140105), immune system process (GO:0002376), cell surface receptor signaling pathway (GO:0007166)
GO Molecular Function (4): IgM binding (GO:0001791), antigen binding (GO:0003823), inhibitory MHC class I receptor activity (GO:0032396), signaling receptor activity (GO:0038023)
GO Cellular Component (3): extracellular region (GO:0005576), plasma membrane (GO:0005886), membrane (GO:0016020)
Reactome top-level categories
Rollup of top-2 pathways:
| Category | Pathways |
|---|---|
| Adaptive Immune System | 1 |
| Immune System | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| positive regulation of cytokine production | 3 |
| immune response | 2 |
| signal transduction | 2 |
| negative regulation of signal transduction | 2 |
| cellular anatomical structure | 2 |
| immune response-activating cell surface receptor signaling pathway | 1 |
| innate immune response-activating signaling pathway | 1 |
| myeloid cell activation involved in immune response | 1 |
| neutrophil activation | 1 |
| regulation of immune response | 1 |
| response to stress | 1 |
| cell communication | 1 |
| cellular process | 1 |
| signaling | 1 |
| regulation of cellular process | 1 |
| cellular response to stimulus | 1 |
| negative regulation of response to biotic stimulus | 1 |
| lipopolysaccharide-mediated signaling pathway | 1 |
| regulation of lipopolysaccharide-mediated signaling pathway | 1 |
| negative regulation of response to external stimulus | 1 |
| granulocyte macrophage colony-stimulating factor production | 1 |
| regulation of granulocyte macrophage colony-stimulating factor production | 1 |
| positive regulation of protein metabolic process | 1 |
| interleukin-1 beta production | 1 |
| regulation of interleukin-1 beta production | 1 |
| positive regulation of interleukin-1 production | 1 |
| interleukin-6 production | 1 |
| regulation of interleukin-6 production | 1 |
| interleukin-8 production | 1 |
| regulation of interleukin-8 production | 1 |
| tumor necrosis factor production | 1 |
| regulation of tumor necrosis factor production | 1 |
| positive regulation of tumor necrosis factor superfamily cytokine production | 1 |
| negative regulation of immune system process | 1 |
| toll-like receptor 4 signaling pathway | 1 |
| regulation of toll-like receptor 4 signaling pathway | 1 |
| defense response to symbiont | 1 |
| cell activation | 1 |
| positive regulation of cellular process | 1 |
| regulation of cell activation | 1 |
Protein interactions and networks
STRING
1216 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| LILRA2 | CD300C | Q08708 | 915 |
| LILRA2 | FCER1G | P30273 | 897 |
| LILRA2 | TYROBP | O43914 | 655 |
| LILRA2 | PTPN6 | P29350 | 592 |
| LILRA2 | RNASE2 | P10153 | 541 |
| LILRA2 | HLA-A | P01891 | 522 |
| LILRA2 | LILRB4 | Q8NHJ6 | 494 |
| LILRA2 | IL10 | P22301 | 494 |
| LILRA2 | CD1B | P29016 | 487 |
| LILRA2 | CD83 | Q01151 | 486 |
| LILRA2 | LAIR1 | Q6GTX8 | 470 |
| LILRA2 | CD1C | P29017 | 447 |
| LILRA2 | PLIN1 | O60240 | 440 |
| LILRA2 | CORO1A | P31146 | 435 |
| LILRA2 | PLIN2 | Q99541 | 435 |
IntAct
5 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| LILRA2 | FCGRT | psi-mi:“MI:0915”(physical association) | 0.400 |
| MOG | LILRA2 | psi-mi:“MI:0915”(physical association) | 0.400 |
| ECE1 | LILRA2 | psi-mi:“MI:0915”(physical association) | 0.370 |
ESM2 similar proteins: A0A0K2S4Q6, A2A7V7, A6NI73, A8K4G0, O43699, O75019, O75022, O75023, O75871, O76036, P0C191, P20138, P24071, P40198, P59901, P80943, Q08708, Q13410, Q28110, Q3U497, Q496F6, Q64JA4, Q6GTX8, Q6ISS4, Q6PI73, Q6UXZ3, Q7TSN2, Q863H2, Q8C567, Q8K249, Q8MJZ2, Q8MJZ7, Q8N149, Q8N423, Q8N6C8, Q8NHJ6, Q8NHL6, Q8VBT3, Q8VCH2, Q95JB9
Diamond homologs: A0A0G2KBC9, A6NI73, C0HJX2, C0HJX3, D3ZQX2, O75019, O75022, O75023, O76036, P0C191, P24071, P43626, P43629, P43630, P59901, P83556, P97484, Q14943, Q14954, Q61450, Q64281, Q6GTX8, Q6ISS4, Q6PI73, Q7TQA1, Q863H2, Q8C567, Q8IYS5, Q8MJZ2, Q8MJZ7, Q8N109, Q8N149, Q8N423, Q8N6C8, Q8N743, Q8NHJ6, Q8NHK3, Q8NHL6, Q95JB9, Q9HCN6
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
141 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 110 |
| Likely benign | 18 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
1200 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 19:54574847:G:GT | donor_gain | 1.0000 |
| 19:54574729:A:AG | acceptor_gain | 0.9900 |
| 19:54574730:G:GG | acceptor_gain | 0.9900 |
| 19:54574730:GGA:G | acceptor_gain | 0.9900 |
| 19:54574848:A:T | donor_gain | 0.9900 |
| 19:54575548:CACAG:C | donor_loss | 0.9900 |
| 19:54575549:ACAG:A | donor_loss | 0.9900 |
| 19:54575552:GGTGA:G | donor_loss | 0.9900 |
| 19:54575553:GT:G | donor_loss | 0.9900 |
| 19:54575554:T:G | donor_loss | 0.9900 |
| 19:54573909:CTCGG:C | donor_loss | 0.9800 |
| 19:54573910:TCGGT:T | donor_loss | 0.9800 |
| 19:54573913:GTG:G | donor_loss | 0.9800 |
| 19:54573914:T:A | donor_loss | 0.9800 |
| 19:54574726:CCTA:C | acceptor_loss | 0.9800 |
| 19:54574728:TA:T | acceptor_loss | 0.9800 |
| 19:54574729:A:AC | acceptor_loss | 0.9800 |
| 19:54574902:G:GA | donor_gain | 0.9800 |
| 19:54575840:AGCC:A | acceptor_gain | 0.9800 |
| 19:54575841:GCCG:G | acceptor_gain | 0.9800 |
| 19:54573915:G:GG | donor_loss | 0.9700 |
| 19:54573978:GTCCC:G | donor_gain | 0.9700 |
| 19:54573979:TCCCT:T | donor_gain | 0.9700 |
| 19:54575032:AGGT:A | donor_loss | 0.9700 |
| 19:54575033:GGTGA:G | donor_loss | 0.9700 |
| 19:54575034:G:GA | donor_loss | 0.9700 |
| 19:54575253:CAGG:C | acceptor_loss | 0.9700 |
| 19:54575254:A:AC | acceptor_loss | 0.9700 |
| 19:54575255:G:GT | acceptor_loss | 0.9700 |
| 19:54575806:GGACA:G | acceptor_gain | 0.9700 |
AlphaMissense
3091 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 19:54575992:T:C | F380L | 0.969 |
| 19:54575994:C:A | F380L | 0.969 |
| 19:54575994:C:G | F380L | 0.969 |
| 19:54575357:T:C | F253L | 0.943 |
| 19:54575359:T:A | F253L | 0.943 |
| 19:54575359:T:G | F253L | 0.943 |
| 19:54574474:T:C | F82L | 0.941 |
| 19:54574476:C:A | F82L | 0.941 |
| 19:54574476:C:G | F82L | 0.941 |
| 19:54575438:T:C | F280L | 0.938 |
| 19:54575440:C:A | F280L | 0.938 |
| 19:54575440:C:G | F280L | 0.938 |
| 19:54575993:T:G | F380C | 0.937 |
| 19:54575911:T:C | F353L | 0.930 |
| 19:54575913:C:A | F353L | 0.930 |
| 19:54575913:C:G | F353L | 0.930 |
| 19:54574375:T:A | C49S | 0.929 |
| 19:54574376:G:C | C49S | 0.929 |
| 19:54575006:A:C | S210R | 0.920 |
| 19:54575008:T:A | S210R | 0.920 |
| 19:54575008:T:G | S210R | 0.920 |
| 19:54576082:A:C | S410R | 0.919 |
| 19:54576084:T:A | S410R | 0.919 |
| 19:54576084:T:G | S410R | 0.919 |
| 19:54575525:A:C | S309R | 0.917 |
| 19:54575527:T:A | S309R | 0.917 |
| 19:54575527:T:G | S309R | 0.917 |
| 19:54574832:T:C | F152L | 0.915 |
| 19:54574834:C:A | F152L | 0.915 |
| 19:54574834:C:G | F152L | 0.915 |
dbSNP variants (sampled 300 via entrez): RS1000101165 (19:54577741 G>A,T), RS1000107535 (19:54573840 C>T), RS1000174357 (19:54585879 T>C), RS1000283635 (19:54579648 A>G), RS1000396759 (19:54581957 C>A,T), RS1000594808 (19:54578129 A>G), RS1000648950 (19:54578332 T>C), RS1000709868 (19:54574675 G>A), RS1000766375 (19:54581723 G>A), RS1000929496 (19:54585782 G>A), RS1000960384 (19:54589042 A>T), RS1001225958 (19:54581614 T>C), RS1001278417 (19:54581828 A>G,T), RS1001289634 (19:54581949 A>C,G), RS1001797543 (19:54586843 T>C)
Disease associations
OMIM: gene MIM:604812 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
0 associations (top):
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
22 total (human), top 22 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Benzo(a)pyrene | decreases expression, increases methylation, affects methylation | 2 |
| Tretinoin | increases expression | 2 |
| triphenyl phosphate | affects expression | 1 |
| tris(2-butoxyethyl) phosphate | affects expression | 1 |
| S-(1,2-dichlorovinyl)cysteine | affects response to substance, increases expression, affects cotreatment, decreases expression | 1 |
| tamibarotene | affects expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| dihydroxy-vitamin D3 | decreases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| MT19c compound | decreases expression | 1 |
| Pioglitazone | decreases expression | 1 |
| Aspirin | decreases expression | 1 |
| Lipopolysaccharides | affects response to substance, increases expression, affects cotreatment, decreases expression | 1 |
| Mercury | decreases expression | 1 |
| Nickel | increases expression | 1 |
| Testosterone | increases expression | 1 |
| Valproic Acid | increases methylation | 1 |
| Cyclosporine | increases expression | 1 |
| Aflatoxin B1 | increases methylation | 1 |
| Antirheumatic Agents | decreases expression | 1 |
| beta-Naphthoflavone | decreases expression | 1 |
| Copper Sulfate | increases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.