ITM2C
gene geneOn this page
Also known as BRI3E25hRPC.1050_D_4ITM3BRICD2C
Summary
ITM2C (integral membrane protein 2C, HGNC:6175) is a protein-coding gene on chromosome 2q37.1, encoding Integral membrane protein 2C (Q9NQX7). Negative regulator of amyloid-beta peptide production.
Enables amyloid-beta binding activity. Involved in negative regulation of neuron projection development and neuron differentiation. Located in several cellular components, including Golgi apparatus; lysosome; and perinuclear region of cytoplasm.
Source: NCBI Gene 81618 — RefSeq curated summary.
At a glance
- GWAS associations: 4
- Clinical variants (ClinVar): 62 total
- MANE Select transcript:
NM_030926
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:6175 |
| Approved symbol | ITM2C |
| Name | integral membrane protein 2C |
| Location | 2q37.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C |
| Ensembl gene | ENSG00000135916 |
| Ensembl biotype | protein_coding |
| OMIM | 609554 |
| Entrez | 81618 |
Gene structure
Transcript identifiers
Ensembl transcripts: 10 — 9 protein_coding, 1 protein_coding_CDS_not_defined
ENST00000326407, ENST00000326427, ENST00000335005, ENST00000409704, ENST00000418408, ENST00000457215, ENST00000492029, ENST00000541852, ENST00000543957, ENST00000620962
RefSeq mRNA: 5 — MANE Select: NM_030926
NM_001012514, NM_001012516, NM_001287240, NM_001287241, NM_030926
CCDS: CCDS2479, CCDS33395, CCDS33396, CCDS74665
Canonical transcript exons
ENST00000326427 — 6 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000922497 | 230877400 | 230877550 |
| ENSE00001868342 | 230878008 | 230879248 |
| ENSE00001899015 | 230864942 | 230865145 |
| ENSE00003548237 | 230873417 | 230873557 |
| ENSE00003611891 | 230875620 | 230875808 |
| ENSE00003784419 | 230876857 | 230876967 |
Expression profiles
Bgee: expression breadth ubiquitous, 275 present calls, max score 99.66.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 164.2906 / max 1966.1830, expressed in 1811 samples.
FANTOM5 promoters (13 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 25828 | 151.3967 | 1793 |
| 25827 | 5.2933 | 1563 |
| 25829 | 2.4477 | 817 |
| 25831 | 1.3348 | 580 |
| 25830 | 0.7148 | 338 |
| 25832 | 0.5243 | 288 |
| 25834 | 0.4790 | 277 |
| 25838 | 0.4667 | 232 |
| 25837 | 0.4142 | 208 |
| 25833 | 0.4096 | 223 |
Top tissues by expression
284 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| nucleus accumbens | UBERON:0001882 | 99.66 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 99.66 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 99.60 | gold quality |
| cingulate cortex | UBERON:0003027 | 99.59 | gold quality |
| caudate nucleus | UBERON:0001873 | 99.56 | gold quality |
| amygdala | UBERON:0001876 | 99.53 | gold quality |
| lateral globus pallidus | UBERON:0002476 | 99.53 | gold quality |
| prefrontal cortex | UBERON:0000451 | 99.47 | gold quality |
| rectum | UBERON:0001052 | 99.47 | gold quality |
| hypothalamus | UBERON:0001898 | 99.46 | gold quality |
| putamen | UBERON:0001874 | 99.42 | gold quality |
| right frontal lobe | UBERON:0002810 | 99.38 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 99.34 | gold quality |
| transverse colon | UBERON:0001157 | 99.28 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 99.17 | gold quality |
| colonic mucosa | UBERON:0000317 | 99.12 | gold quality |
| pituitary gland | UBERON:0000007 | 99.11 | gold quality |
| frontal cortex | UBERON:0001870 | 99.09 | gold quality |
| adenohypophysis | UBERON:0002196 | 99.09 | gold quality |
| mucosa of sigmoid colon | UBERON:0004993 | 99.09 | gold quality |
| neocortex | UBERON:0001950 | 99.01 | gold quality |
| forebrain | UBERON:0001890 | 98.97 | gold quality |
| Ammon’s horn | UBERON:0001954 | 98.97 | gold quality |
| telencephalon | UBERON:0001893 | 98.96 | gold quality |
| substantia nigra | UBERON:0002038 | 98.93 | gold quality |
| spinal cord | UBERON:0002240 | 98.90 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 98.88 | gold quality |
| midbrain | UBERON:0001891 | 98.85 | gold quality |
| temporal lobe | UBERON:0001871 | 98.83 | gold quality |
| substantia nigra pars reticulata | UBERON:0001966 | 98.83 | gold quality |
Single-cell (SCXA)
Detected in 46 experiment(s), a significant marker in 38.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-125970 | yes | 2451.42 |
| E-CURD-120 | yes | 1734.99 |
| E-MTAB-9467 | yes | 1551.01 |
| E-HCAD-10 | yes | 1520.22 |
| E-GEOD-150728 | yes | 1467.01 |
| E-GEOD-149689 | yes | 1438.55 |
| E-MTAB-8410 | yes | 1325.94 |
| E-MTAB-9154 | yes | 1319.79 |
| E-HCAD-32 | yes | 1300.46 |
| E-CURD-77 | yes | 1223.15 |
| E-MTAB-7407 | yes | 1138.29 |
| E-HCAD-4 | yes | 1017.62 |
| E-MTAB-10553 | yes | 899.47 |
| E-CURD-55 | yes | 852.80 |
| E-MTAB-9221 | yes | 826.07 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
74 targeting ITM2C, 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-LET-7A-3P | 100.00 | 74.03 | 3932 |
| HSA-LET-7B-3P | 100.00 | 74.08 | 3913 |
| HSA-LET-7F-1-3P | 100.00 | 74.02 | 3928 |
| HSA-MIR-98-3P | 100.00 | 74.08 | 3907 |
| HSA-MIR-9-5P | 100.00 | 72.28 | 2361 |
| HSA-MIR-6798-5P | 100.00 | 65.77 | 699 |
| HSA-MIR-5196-5P | 100.00 | 67.98 | 2761 |
| HSA-MIR-1252-5P | 100.00 | 69.80 | 2774 |
| HSA-MIR-4531 | 99.99 | 69.70 | 3181 |
| HSA-MIR-520D-5P | 99.98 | 73.34 | 4883 |
| HSA-MIR-524-5P | 99.98 | 73.43 | 4882 |
| HSA-MIR-4666A-3P | 99.96 | 71.71 | 3434 |
| HSA-MIR-6721-5P | 99.93 | 68.92 | 2981 |
| HSA-MIR-218-5P | 99.93 | 72.22 | 2103 |
| HSA-MIR-381-3P | 99.93 | 71.87 | 2854 |
| HSA-MIR-300 | 99.92 | 71.76 | 2856 |
| HSA-MIR-205-3P | 99.92 | 69.92 | 3165 |
| HSA-MIR-4648 | 99.91 | 67.00 | 710 |
| HSA-MIR-627-3P | 99.90 | 71.42 | 3316 |
| HSA-MIR-605-3P | 99.88 | 69.22 | 1833 |
| HSA-MIR-4492 | 99.87 | 68.25 | 3611 |
| HSA-MIR-12119 | 99.87 | 68.35 | 1653 |
| HSA-MIR-659-3P | 99.85 | 70.69 | 1620 |
| HSA-MIR-636 | 99.80 | 69.58 | 1500 |
| HSA-MIR-548AJ-5P | 99.78 | 71.12 | 3085 |
| HSA-MIR-548F-5P | 99.78 | 71.02 | 3093 |
| HSA-MIR-548G-5P | 99.78 | 71.12 | 3085 |
| HSA-MIR-548X-5P | 99.78 | 71.12 | 3085 |
| HSA-MIR-1976 | 99.74 | 65.48 | 1127 |
| HSA-MIR-4306 | 99.72 | 70.50 | 3630 |
Literature-anchored findings (GeneRIF, showing 1)
- Unlocking the Potential of the CA2, CA7, and ITM2C Gene Signatures for the Early Detection of Colorectal Cancer: A Comprehensive Analysis of RNA-Seq Data by Utilizing Machine Learning Algorithms. (PMID:37895185)
Cross-species orthologs
6 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | itm2cb | ENSDARG00000039650 |
| danio_rerio | itm2ca | ENSDARG00000043448 |
| mus_musculus | Itm2c | ENSMUSG00000026223 |
| rattus_norvegicus | Itm2c | ENSRNOG00000017359 |
| drosophila_melanogaster | CG3662 | FBGN0031285 |
| caenorhabditis_elegans | WBGENE00016106 |
Paralogs (2): ITM2A (ENSG00000078596), ITM2B (ENSG00000136156)
Protein
Protein identifiers
Integral membrane protein 2C — Q9NQX7 (reviewed: Q9NQX7)
Alternative names: Cerebral protein 14, Transmembrane protein BRI3
All UniProt accessions (6): B8ZZM6, C9JG41, E7EUS6, F5H4I5, Q96JS4, Q9NQX7
UniProt curated annotations — full annotation on UniProt →
Function. Negative regulator of amyloid-beta peptide production. May inhibit the processing of APP by blocking its access to alpha- and beta-secretase. Binding to the beta-secretase-cleaved APP C-terminal fragment is negligible, suggesting that ITM2C is a poor gamma-secretase cleavage inhibitor. May play a role in TNF-induced cell death and neuronal differentiation.
Subunit / interactions. Interacts with BACE1. Interacts with APP. Interacts with STMN2.
Subcellular location. Lysosome membrane. Cell membrane.
Tissue specificity. High levels in the brain, specifically in the cerebral cortex, medulla, amygdala, hippocampus, thalamus, caudate nucleus, cerebellum, olfactory lobe and spinal cord. Very low levels in other organs.
Post-translational modifications. Type I membrane-bound, as well as soluble, furin has a pre-eminent role in ITM2C proteolytic processing. PCSK7 and PCSK5 may also be involved although to a lesser extent. The soluble form of PCSK7 is incapable of processing ITM2C. Fails to undergo shedding by ADAM10 and intramembrane cleavage by SPPL2B.
Similarity. Belongs to the ITM2 family.
Isoforms (3)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q9NQX7-1 | 1 | yes |
| Q9NQX7-2 | 2 | |
| Q9NQX7-3 | 3 |
RefSeq proteins (5): NP_001012532, NP_001012534, NP_001274169, NP_001274170, NP_112188* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR007084 | BRICHOS_dom | Domain |
| IPR040145 | ITM2 | Family |
Pfam: PF04089
UniProt features (15 total): sequence conflict 3, splice variant 2, chain 1, peptide 1, sequence variant 1, mutagenesis site 1, transmembrane region 1, domain 1, site 1, modified residue 1, glycosylation site 1, disulfide bond 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9NQX7-F1 | 77.12 | 0.42 |
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 (1): 242–243 (cleavage; by furin)
Post-translational modifications (1): 37
Disulfide bonds (1): 163–222
Glycosylation sites (1): 169
Mutagenesis-validated functional residues (1):
| Position | Phenotype |
|---|---|
| 241–242 | completely abrogates proteolytic processing. |
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 488 (showing top):
GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, VERHAAK_AML_WITH_NPM1_MUTATED_DN, REACTOME_INNATE_IMMUNE_SYSTEM, MODULE_255, GOCC_VACUOLAR_MEMBRANE, GOCC_SECRETORY_GRANULE, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, MODULE_317, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, GOBP_NEUROGENESIS, HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION
GO Biological Process (4): negative regulation of neuron projection development (GO:0010977), neuron differentiation (GO:0030182), negative regulation of amyloid precursor protein biosynthetic process (GO:0042985), positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)
GO Molecular Function (3): amyloid-beta binding (GO:0001540), ATP binding (GO:0005524), protein binding (GO:0005515)
GO Cellular Component (7): lysosome (GO:0005764), lysosomal membrane (GO:0005765), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), perinuclear region of cytoplasm (GO:0048471), extracellular exosome (GO:0070062), membrane (GO:0016020)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cytoplasm | 2 |
| cellular anatomical structure | 2 |
| regulation of neuron projection development | 1 |
| neuron projection development | 1 |
| negative regulation of cell projection organization | 1 |
| cell differentiation | 1 |
| generation of neurons | 1 |
| negative regulation of glycoprotein biosynthetic process | 1 |
| amyloid precursor protein biosynthetic process | 1 |
| regulation of amyloid precursor protein biosynthetic process | 1 |
| extrinsic apoptotic signaling pathway | 1 |
| positive regulation of apoptotic signaling pathway | 1 |
| regulation of extrinsic apoptotic signaling pathway | 1 |
| peptide binding | 1 |
| adenyl ribonucleotide binding | 1 |
| purine ribonucleoside triphosphate binding | 1 |
| binding | 1 |
| lytic vacuole | 1 |
| lysosome | 1 |
| lytic vacuole membrane | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
| membrane | 1 |
| cell periphery | 1 |
| extracellular vesicle | 1 |
Protein interactions and networks
STRING
1026 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| ITM2C | BACE1 | P56817 | 752 |
| ITM2C | PCSK7 | Q16549 | 748 |
| ITM2C | CLPTM1 | O96005 | 611 |
| ITM2C | FURIN | P09958 | 589 |
| ITM2C | SLC35A5 | Q9BS91 | 525 |
| ITM2C | KNDC1 | Q76NI1 | 513 |
| ITM2C | KIAA1755 | Q5JYT7 | 454 |
| ITM2C | PDZD11 | Q5EBL8 | 431 |
| ITM2C | INSYN1 | Q2T9L4 | 410 |
| ITM2C | ERBB2 | P04626 | 399 |
| ITM2C | SYT11 | Q9BT88 | 391 |
| ITM2C | EPB41L4A | Q9HCS5 | 388 |
| ITM2C | MED31 | Q9Y3C7 | 371 |
| ITM2C | EML6 | Q6ZMW3 | 363 |
| ITM2C | GAS2L3 | Q86XJ1 | 359 |
IntAct
75 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| TSPAN15 | ADAM10 | psi-mi:“MI:0914”(association) | 0.840 |
| TSPAN5 | ADAM10 | psi-mi:“MI:0914”(association) | 0.800 |
| APP | APBB1 | psi-mi:“MI:0914”(association) | 0.740 |
| CFTR | ESYT2 | psi-mi:“MI:2364”(proximity) | 0.710 |
| SLC39A5 | FAM171A2 | psi-mi:“MI:0914”(association) | 0.640 |
| MTNR1B | IRS4 | psi-mi:“MI:0914”(association) | 0.530 |
| TNFSF8 | LGALS8 | psi-mi:“MI:0914”(association) | 0.530 |
| TIMP3 | ZZEF1 | psi-mi:“MI:0914”(association) | 0.530 |
| ANKH | FAM234B | psi-mi:“MI:0914”(association) | 0.530 |
| CFTR | ITM2C | psi-mi:“MI:0915”(physical association) | 0.520 |
| NRAS | ESYT2 | psi-mi:“MI:2364”(proximity) | 0.480 |
| ITM2C | Dlg4 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| RNF7 | ITM2C | psi-mi:“MI:0915”(physical association) | 0.370 |
| psi-mi:“MI:0914”(association) | 0.350 | ||
| ESYT2 | psi-mi:“MI:0914”(association) | 0.350 | |
| PGRMC1 | psi-mi:“MI:0914”(association) | 0.350 | |
| SNAP23 | psi-mi:“MI:0914”(association) | 0.350 | |
| HAX1 | psi-mi:“MI:0914”(association) | 0.350 | |
| APP | RTL1 | psi-mi:“MI:0914”(association) | 0.350 |
| M | psi-mi:“MI:0914”(association) | 0.350 | |
| NS3 | C15orf61 | psi-mi:“MI:0914”(association) | 0.350 |
| SHTN1 | psi-mi:“MI:0914”(association) | 0.350 | |
| TMEM223 | psi-mi:“MI:0914”(association) | 0.350 | |
| TNFRSF10A | psi-mi:“MI:0914”(association) | 0.350 | |
| POMK | ESYT2 | psi-mi:“MI:0914”(association) | 0.350 |
| SCN2A | IGLL5 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (134): ITM2C (Affinity Capture-MS), MVB12B (Affinity Capture-MS), ITM2C (Two-hybrid), ITM2C (Proximity Label-MS), ITM2C (Proximity Label-MS), MVB12B (Affinity Capture-MS), ITM2C (Reconstituted Complex), ITM2C (Proximity Label-MS), ITM2C (Proximity Label-MS), ITM2C (Proximity Label-MS), ITM2C (Affinity Capture-MS), ITM2C (Two-hybrid), ITM2C (Two-hybrid), CXCL9 (Two-hybrid), FNDC9 (Two-hybrid)
ESM2 similar proteins: A2VDN0, A5A6H8, B5DFM7, E9Q9F6, O18638, O42204, O43736, O88393, O89051, P0DP43, P21841, P26342, P58239, Q03167, Q06890, Q06AV4, Q14CH0, Q29TV8, Q3T0P7, Q4R540, Q52N47, Q5NVC3, Q5PQL7, Q5R876, Q5SC59, Q5SC60, Q5SY80, Q5XIE8, Q60HC1, Q61500, Q6AYE5, Q6GPK2, Q6P7C7, Q6P995, Q6W3E5, Q71SY6, Q802A9, Q86XM0, Q86XP6, Q8BGN6
Diamond homologs: A2VDN0, A5A6H8, O42204, O43736, O89051, Q06AV4, Q3T0P7, Q4R540, Q52N47, Q5NVC3, Q5PQL7, Q5R876, Q5XIE8, Q60HC1, Q61500, Q91VK4, Q9NQX7, Q9Y287
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
62 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 39 |
| Likely benign | 2 |
| Benign | 2 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
885 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 2:230865144:GG:G | donor_gain | 1.0000 |
| 2:230865145:GG:G | donor_gain | 1.0000 |
| 2:230865146:G:GG | donor_gain | 1.0000 |
| 2:230875608:C:CA | acceptor_gain | 1.0000 |
| 2:230875613:T:TA | acceptor_gain | 1.0000 |
| 2:230875617:CAG:C | acceptor_loss | 1.0000 |
| 2:230875618:A:AG | acceptor_gain | 1.0000 |
| 2:230875618:AGC:A | acceptor_loss | 1.0000 |
| 2:230875618:AGCT:A | acceptor_gain | 1.0000 |
| 2:230875618:AGCTG:A | acceptor_gain | 1.0000 |
| 2:230875619:G:GA | acceptor_gain | 1.0000 |
| 2:230875619:GC:G | acceptor_gain | 1.0000 |
| 2:230875619:GCT:G | acceptor_gain | 1.0000 |
| 2:230875619:GCTG:G | acceptor_gain | 1.0000 |
| 2:230875619:GCTGG:G | acceptor_gain | 1.0000 |
| 2:230875805:GCGG:G | donor_gain | 1.0000 |
| 2:230875807:GG:G | donor_gain | 1.0000 |
| 2:230875808:GG:G | donor_gain | 1.0000 |
| 2:230875809:G:GG | donor_gain | 1.0000 |
| 2:230875809:GTG:G | donor_loss | 1.0000 |
| 2:230875810:T:A | donor_loss | 1.0000 |
| 2:230876852:GCCA:G | acceptor_loss | 1.0000 |
| 2:230876853:CCAG:C | acceptor_loss | 1.0000 |
| 2:230876854:CA:C | acceptor_loss | 1.0000 |
| 2:230876855:A:AC | acceptor_loss | 1.0000 |
| 2:230876855:A:AG | acceptor_gain | 1.0000 |
| 2:230876855:AG:A | acceptor_gain | 1.0000 |
| 2:230876855:AGG:A | acceptor_gain | 1.0000 |
| 2:230876856:G:GT | acceptor_gain | 1.0000 |
| 2:230876856:GG:G | acceptor_gain | 1.0000 |
AlphaMissense
1738 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 2:230875800:T:C | F148L | 1.000 |
| 2:230875801:T:G | F148C | 1.000 |
| 2:230875802:C:A | F148L | 1.000 |
| 2:230875802:C:G | F148L | 1.000 |
| 2:230875794:C:G | H146D | 0.999 |
| 2:230875801:T:C | F148S | 0.999 |
| 2:230876861:T:C | L152P | 0.999 |
| 2:230876866:G:C | A154P | 0.999 |
| 2:230876869:T:G | Y155D | 0.999 |
| 2:230876893:T:A | C163S | 0.999 |
| 2:230876893:T:C | C163R | 0.999 |
| 2:230876894:G:A | C163Y | 0.999 |
| 2:230876894:G:C | C163S | 0.999 |
| 2:230876894:G:T | C163F | 0.999 |
| 2:230876895:C:G | C163W | 0.999 |
| 2:230876900:T:A | V165D | 0.999 |
| 2:230876909:T:A | L168H | 0.999 |
| 2:230877502:T:A | C222S | 0.999 |
| 2:230877502:T:C | C222R | 0.999 |
| 2:230877503:G:A | C222Y | 0.999 |
| 2:230877503:G:C | C222S | 0.999 |
| 2:230877503:G:T | C222F | 0.999 |
| 2:230877504:C:G | C222W | 0.999 |
| 2:230875789:T:A | I144N | 0.998 |
| 2:230875789:T:C | I144T | 0.998 |
| 2:230875789:T:G | I144S | 0.998 |
| 2:230875795:A:C | H146P | 0.998 |
| 2:230875796:T:A | H146Q | 0.998 |
| 2:230875796:T:G | H146Q | 0.998 |
| 2:230875798:A:C | D147A | 0.998 |
dbSNP variants (sampled 300 via entrez): RS1000416614 (2:230868292 G>A), RS1000548826 (2:230864035 G>A,T), RS1000571796 (2:230870165 G>A), RS1000972729 (2:230875151 C>A), RS1000996914 (2:230864399 G>A,T), RS1001151902 (2:230869399 C>T), RS1001178782 (2:230871137 G>T), RS1001228166 (2:230865844 C>T), RS1001229758 (2:230873684 C>T), RS1001233646 (2:230865482 TGGGG>T,TGGG,TGGGGG), RS1001279224 (2:230866017 G>A,C,T), RS1001297753 (2:230877750 T>C), RS1001682952 (2:230868961 C>A), RS1001702041 (2:230873863 G>A), RS1001736680 (2:230868745 C>T)
Disease associations
OMIM: gene MIM:609554 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
4 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST90002390_468 | Mean corpuscular hemoglobin | 2.000000e-12 |
| GCST90002392_176 | Mean corpuscular volume | 7.000000e-13 |
| GCST90002396_183 | Mean reticulocyte volume | 1.000000e-09 |
| GCST90002397_464 | Mean spheric corpuscular volume | 7.000000e-11 |
EFO canonical traits (2, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004527 | mean corpuscular hemoglobin |
| EFO:0010701 | mean reticulocyte volume |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
43 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| bisphenol A | increases methylation, decreases expression, affects expression, affects cotreatment | 4 |
| Arsenic | affects methylation, decreases ubiquitination, increases methylation, decreases expression, increases abundance | 4 |
| Valproic Acid | affects expression, increases expression, increases methylation | 4 |
| sodium arsenite | decreases expression, increases abundance, increases expression | 2 |
| Benzo(a)pyrene | affects methylation, increases expression | 2 |
| Phenylmercuric Acetate | affects cotreatment, increases expression | 2 |
| Cyclosporine | decreases expression | 2 |
| TAK-243 | increases sumoylation | 1 |
| lead acetate | increases expression | 1 |
| beta-lapachone | decreases expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | decreases expression | 1 |
| 2-bromopalmitate | decreases reaction, increases abundance, increases palmitoylation | 1 |
| beta-methylcholine | affects expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, increases expression | 1 |
| ICG 001 | increases expression | 1 |
| abrine | decreases expression | 1 |
| dorsomorphin | affects cotreatment, increases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| MT19c compound | decreases expression | 1 |
| Fulvestrant | increases methylation, affects cotreatment | 1 |
| Acetaminophen | increases expression | 1 |
| Atrazine | increases expression | 1 |
| Cadmium | decreases reaction, increases abundance, increases palmitoylation | 1 |
| Cytarabine | decreases expression | 1 |
| Dichlorodiphenyl Dichloroethylene | decreases expression | 1 |
| Doxorubicin | increases expression | 1 |
| Estradiol | affects cotreatment, decreases expression | 1 |
| Gallic Acid | decreases expression | 1 |
| Ivermectin | decreases expression | 1 |
| Lead | affects expression | 1 |
Cellosaurus cell lines
1 cell lines: 1 cancer cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_E0FM | Ubigene HeLa ITM2C KO | Cancer cell line | Female |
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.