HOXC11
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Summary
HOXC11 (homeobox C11, HGNC:5123) is a protein-coding gene on chromosome 12q13.13, encoding Homeobox protein Hox-C11 (O43248). Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.
This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXC genes located in a cluster on chromosome 12. The product of this gene binds to a promoter element of the lactase-phlorizin hydrolase. It also may play a role in early intestinal development. An alternatively spliced variant encoding a shorter isoform has been described but its full-length nature has not been determined.
Source: NCBI Gene 3227 — RefSeq curated summary.
At a glance
- GWAS associations: 5
- Clinical variants (ClinVar): 10 total
- MANE Select transcript:
NM_014212
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:5123 |
| Approved symbol | HOXC11 |
| Name | homeobox C11 |
| Location | 12q13.13 |
| Locus type | gene with protein product |
| Status | Approved |
| Ensembl gene | ENSG00000123388 |
| Ensembl biotype | protein_coding |
| OMIM | 605559 |
| Entrez | 3227 |
Gene structure
Transcript identifiers
Ensembl transcripts: 2 — 2 protein_coding
ENST00000243082, ENST00000546378
RefSeq mRNA: 1 — MANE Select: NM_014212
NM_014212
CCDS: CCDS8867
Canonical transcript exons
ENST00000546378 — 2 exons
| Exon | Start | End |
|---|---|---|
| ENSE00002343306 | 53973126 | 53973923 |
| ENSE00002362919 | 53975181 | 53977643 |
Expression profiles
Bgee: expression breadth broad, 63 present calls, max score 97.04.
FANTOM5 (CAGE): breadth broad, TPM avg 1.0850 / max 211.0531, expressed in 203 samples.
FANTOM5 promoters (6 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 125822 | 0.3865 | 126 |
| 125821 | 0.2632 | 109 |
| 125820 | 0.2497 | 65 |
| 125823 | 0.1149 | 65 |
| 125818 | 0.0646 | 23 |
| 125819 | 0.0062 | 2 |
Top tissues by expression
273 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 97.04 | gold quality |
| type B pancreatic cell | CL:0000169 | 78.14 | gold quality |
| olfactory bulb | UBERON:0002264 | 76.65 | gold quality |
| diaphragm | UBERON:0001103 | 74.69 | gold quality |
| skin of leg | UBERON:0001511 | 73.34 | gold quality |
| popliteal artery | UBERON:0002250 | 73.18 | gold quality |
| tibial artery | UBERON:0007610 | 73.14 | gold quality |
| mucosa of paranasal sinus | UBERON:0005030 | 72.48 | gold quality |
| endometrium epithelium | UBERON:0004811 | 72.43 | gold quality |
| vastus lateralis | UBERON:0001379 | 70.20 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 70.00 | gold quality |
| zone of skin | UBERON:0000014 | 69.97 | gold quality |
| quadriceps femoris | UBERON:0001377 | 69.82 | gold quality |
| hair follicle | UBERON:0002073 | 69.44 | gold quality |
| superficial temporal artery | UBERON:0001614 | 69.17 | gold quality |
| skeletal muscle tissue of rectus abdominis | UBERON:0004511 | 68.34 | gold quality |
| skin of abdomen | UBERON:0001416 | 68.21 | gold quality |
| tibialis anterior | UBERON:0001385 | 66.70 | silver quality |
| pancreatic ductal cell | CL:0002079 | 66.55 | silver quality |
| cerebellar vermis | UBERON:0004720 | 65.71 | gold quality |
| decidua | UBERON:0002450 | 65.55 | gold quality |
| epithelium of nasopharynx | UBERON:0001951 | 65.28 | gold quality |
| thymus | UBERON:0002370 | 65.13 | gold quality |
| saphenous vein | UBERON:0007318 | 65.13 | silver quality |
| cardia of stomach | UBERON:0001162 | 64.88 | gold quality |
| layer of synovial tissue | UBERON:0007616 | 64.81 | gold quality |
| dorsal plus ventral thalamus | UBERON:0001897 | 64.30 | gold quality |
| subthalamic nucleus | UBERON:0001906 | 64.20 | gold quality |
| inferior vagus X ganglion | UBERON:0005363 | 63.99 | gold quality |
| ventral tegmental area | UBERON:0002691 | 63.75 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 0.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 1.14 |
Regulation
Is transcription factor: yes
Downstream targets (CollecTRI)
4 targets.
| Target | Regulation |
|---|---|
| CD24 | |
| LCT | Unknown |
| PAWR | Repression |
| S100B | Unknown |
JASPAR motifs
| Motif | Name | Family |
|---|---|---|
| MA0651.1 | HOXC11 | HOX |
| MA0651.2 | HOXC11 | HOX |
| MA0651.3 | HOXC11 | HOX |
JASPAR matrix evidence (PMIDs): PMID:18585359
Upstream regulators (CollecTRI, top): KDM6A, PITX1
miRNA regulators (miRDB)
37 targeting HOXC11, 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-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-513A-5P | 100.00 | 69.77 | 2465 |
| HSA-MIR-3064-3P | 100.00 | 70.09 | 1254 |
| HSA-MIR-5196-5P | 100.00 | 67.98 | 2761 |
| HSA-MIR-4776-3P | 100.00 | 68.73 | 1340 |
| HSA-MIR-6798-5P | 100.00 | 65.77 | 699 |
| HSA-MIR-4747-5P | 100.00 | 67.90 | 2681 |
| HSA-MIR-12121 | 99.99 | 66.64 | 255 |
| HSA-MIR-6870-5P | 99.99 | 68.55 | 2115 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-4715-3P | 99.98 | 66.03 | 670 |
| HSA-MIR-27A-3P | 99.98 | 72.13 | 2955 |
| HSA-MIR-27B-3P | 99.98 | 72.13 | 2955 |
| HSA-MIR-9985 | 99.98 | 72.11 | 2939 |
| 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-3148 | 99.97 | 75.06 | 6478 |
| HSA-MIR-92A-2-5P | 99.75 | 67.01 | 2164 |
| HSA-MIR-4699-3P | 99.71 | 70.15 | 3142 |
| HSA-MIR-4261 | 99.59 | 70.30 | 3415 |
| HSA-MIR-3120-3P | 99.54 | 70.28 | 2669 |
| HSA-MIR-642A-5P | 99.51 | 65.10 | 1152 |
| HSA-MIR-217-5P | 99.49 | 69.93 | 1419 |
| HSA-MIR-147B-5P | 99.45 | 70.62 | 2432 |
| HSA-MIR-513A-3P | 99.39 | 70.63 | 3620 |
| HSA-MIR-513C-3P | 99.39 | 70.63 | 3620 |
| HSA-MIR-3978 | 99.24 | 68.39 | 2201 |
| HSA-MIR-122B-3P | 99.21 | 68.90 | 1333 |
| HSA-MIR-21-3P | 99.21 | 68.95 | 1312 |
Literature-anchored findings (GeneRIF, showing 7)
- HOXC11 increases transcription of S100beta gene in BrdU-induced in vitro differentiation of GOTO neuroblastoma cells into Schwann cells. (PMID:17488478)
- HOXC11 and SRC-1 cooperate to regulate expression of the calcium-binding protein S100beta in resistant breast cancer cells. (PMID:20145129)
- Our data suggest that HOXC11 may contribute to RCC carcinogenesis by increasing tumor cell proliferation and imply that HOXC11 may be an important determinant of RCC patient prognosis (PMID:25476856)
- MiR-1197 was upregulated in non-small cell lung cancer (NSCLC) and its downregulation has tumor-suppressing effects in NSCLC, very likely through inverse regulation on downstream target gene of HOXC11. (PMID:31181445)
- HOXC11 was up-regulated and closely correlated with overall patient survival in colon adenocarcinoma and kidney renal clear cell carcinoma. (PMID:31923422)
- HOXC11 Expression Is Associated with the Progression of Colon Adenocarcinoma and Is a Prognostic Biomarker. (PMID:34415792)
- HOXC11 drives lung adenocarcinoma progression through transcriptional regulation of SPHK1. (PMID:36823149)
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | hoxc11a | ENSDARG00000070351 |
| mus_musculus | Hoxc11 | ENSMUSG00000001656 |
| rattus_norvegicus | Hoxc11 | ENSRNOG00000016141 |
Paralogs (42): HOXA11 (ENSG00000005073), HOXC8 (ENSG00000037965), HOXA1 (ENSG00000105991), HOXA2 (ENSG00000105996), HOXA3 (ENSG00000105997), HOXA5 (ENSG00000106004), HOXA6 (ENSG00000106006), HOXA13 (ENSG00000106031), TLX1 (ENSG00000107807), HOXB6 (ENSG00000108511), TLX2 (ENSG00000115297), HOXB8 (ENSG00000120068), HOXB5 (ENSG00000120075), HOXB3 (ENSG00000120093), HOXB1 (ENSG00000120094), HOXA7 (ENSG00000122592), HOXC13 (ENSG00000123364), HOXC12 (ENSG00000123407), HOXD1 (ENSG00000128645), HOXD3 (ENSG00000128652), HOXD9 (ENSG00000128709), HOXD10 (ENSG00000128710), HOXD11 (ENSG00000128713), HOXD13 (ENSG00000128714), PDX1 (ENSG00000139515), HOXB13 (ENSG00000159184), TLX3 (ENSG00000164438), HOXD4 (ENSG00000170166), HOXD12 (ENSG00000170178), HOXB9 (ENSG00000170689), HOXC5 (ENSG00000172789), HOXB2 (ENSG00000173917), HOXD8 (ENSG00000175879), GSX2 (ENSG00000180613), HOXC9 (ENSG00000180806), HOXC10 (ENSG00000180818), HOXB4 (ENSG00000182742), HOXA4 (ENSG00000197576), HOXC6 (ENSG00000197757), HOXC4 (ENSG00000198353)
Protein
Protein identifiers
Homeobox protein Hox-C11 — O43248 (reviewed: O43248)
Alternative names: Homeobox protein Hox-3H
All UniProt accessions (2): O43248, J3KMZ0
UniProt curated annotations — full annotation on UniProt →
Function. Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Binds to a promoter element of the lactase-phlorizin hydrolase gene.
Subcellular location. Nucleus.
Similarity. Belongs to the Abd-B homeobox family.
RefSeq proteins (1): NP_055027* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR001356 | HD | Domain |
| IPR009057 | Homeodomain-like_sf | Homologous_superfamily |
| IPR017970 | Homeobox_CS | Conserved_site |
| IPR020479 | HD_metazoa | Domain |
| IPR021918 | DUF3528 | Domain |
Pfam: PF00046, PF12045
UniProt features (9 total): cross-link 3, sequence variant 2, chain 1, DNA-binding region 1, region of interest 1, sequence conflict 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-O43248-F1 | 61.31 | 0.21 |
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 (3): 82, 116, 178
Function
Pathways and Gene Ontology
Reactome pathways
1 pathways
| ID | Pathway |
|---|---|
| R-HSA-9830674 | Formation of the ureteric bud |
MSigDB gene sets: 180 (showing top):
RNGTGGGC_UNKNOWN, MYAATNNNNNNNGGC_UNKNOWN, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, BENPORATH_ES_WITH_H3K27ME3, GOBP_METANEPHROS_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_EMBRYONIC_DIGIT_MORPHOGENESIS, GOBP_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_MORPHOGENESIS, GOBP_DEVELOPMENTAL_INDUCTION, GGGTGGRR_PAX4_03, USF_C, MORF_RAD51L3, TCF4_Q5
GO Biological Process (11): metanephros development (GO:0001656), organ induction (GO:0001759), regulation of transcription by RNA polymerase II (GO:0006357), endoderm development (GO:0007492), anterior/posterior pattern specification (GO:0009952), proximal/distal pattern formation (GO:0009954), embryonic digit morphogenesis (GO:0042733), positive regulation of transcription by RNA polymerase II (GO:0045944), embryonic skeletal joint morphogenesis (GO:0060272), skeletal system development (GO:0001501), regulation of DNA-templated transcription (GO:0006355)
GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515)
GO Cellular Component (4): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829)
Reactome top-level categories
Rollup of top-1 pathways:
| Category | Pathways |
|---|---|
| Kidney development | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| RNA polymerase II transcription regulatory region sequence-specific DNA binding | 3 |
| cellular anatomical structure | 3 |
| transcription by RNA polymerase II | 2 |
| regionalization | 2 |
| regulation of transcription by RNA polymerase II | 2 |
| kidney development | 1 |
| regulation of animal organ formation | 1 |
| specification of animal organ identity | 1 |
| developmental induction | 1 |
| positive regulation of animal organ morphogenesis | 1 |
| regulation of DNA-templated transcription | 1 |
| tissue development | 1 |
| embryonic limb morphogenesis | 1 |
| embryonic morphogenesis | 1 |
| positive regulation of DNA-templated transcription | 1 |
| embryonic skeletal system morphogenesis | 1 |
| embryonic skeletal joint development | 1 |
| system development | 1 |
| DNA-templated transcription | 1 |
| regulation of gene expression | 1 |
| regulation of RNA biosynthetic process | 1 |
| cis-regulatory region sequence-specific DNA binding | 1 |
| chromatin | 1 |
| DNA-binding transcription factor activity | 1 |
| DNA-binding transcription factor activity, RNA polymerase II-specific | 1 |
| DNA-binding transcription activator activity | 1 |
| positive regulation of transcription by RNA polymerase II | 1 |
| double-stranded DNA binding | 1 |
| sequence-specific DNA binding | 1 |
| nucleic acid binding | 1 |
| binding | 1 |
| chromosome | 1 |
| intracellular membrane-bounded organelle | 1 |
| nuclear lumen | 1 |
| cytoplasm | 1 |
Protein interactions and networks
STRING
686 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| HOXC11 | TBX4 | P57082 | 842 |
| HOXC11 | TBX5 | Q99593 | 724 |
| HOXC11 | TBX3 | O15119 | 580 |
| HOXC11 | TBX6 | O95947 | 580 |
| HOXC11 | TBX2 | Q13207 | 571 |
| HOXC11 | SALL4 | Q9UJQ4 | 567 |
| HOXC11 | DUX4L2 | P0CJ85 | 554 |
| HOXC11 | EYA1 | Q99502 | 545 |
| HOXC11 | PAX2 | Q02962 | 509 |
| HOXC11 | HOXC5 | Q00444 | 480 |
| HOXC11 | TBR1 | Q16650 | 470 |
| HOXC11 | GAPDH | P00354 | 458 |
| HOXC11 | SRC | P12931 | 453 |
| HOXC11 | TBX1 | O43435 | 450 |
| HOXC11 | ATP2A2 | P16614 | 411 |
IntAct
41 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| HOXC11 | HTT | psi-mi:“MI:0915”(physical association) | 0.670 |
| HOXC11 | TRIP10 | psi-mi:“MI:0915”(physical association) | 0.560 |
| HOXC11 | PSMA1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| HOXC11 | psi-mi:“MI:0915”(physical association) | 0.560 | |
| HOXC11 | FGFR3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| HOXC11 | HRAS | psi-mi:“MI:0915”(physical association) | 0.560 |
| HOXC11 | PMP22 | psi-mi:“MI:0915”(physical association) | 0.560 |
| HOXC11 | HDAC5 | psi-mi:“MI:0915”(physical association) | 0.370 |
| HOXC11 | GTF2A1L | psi-mi:“MI:0915”(physical association) | 0.370 |
| HOXC11 | TBX21 | psi-mi:“MI:0915”(physical association) | 0.370 |
| HOXC11 | SOX8 | psi-mi:“MI:0915”(physical association) | 0.370 |
| GTF2H1 | HOXC11 | psi-mi:“MI:0915”(physical association) | 0.370 |
| HOXC11 | IRF4 | psi-mi:“MI:0915”(physical association) | 0.370 |
| HOXC11 | SMAD3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| HOXC11 | MEIS1 | psi-mi:“MI:0915”(physical association) | 0.370 |
| HOXC11 | SP1 | psi-mi:“MI:0915”(physical association) | 0.370 |
BioGRID (23): HOXC11 (Reconstituted Complex), HOXC11 (Affinity Capture-MS), RCHY1 (PCA), TRIP10 (Two-hybrid), PSMA1 (Two-hybrid), HOXC11 (Affinity Capture-RNA), HOXC11 (Affinity Capture-MS), HOXC11 (Affinity Capture-MS), HOXC11 (Proximity Label-MS), HOXC11 (Proximity Label-MS), HOXC11 (Two-hybrid), IRF4 (Two-hybrid), SMAD3 (Two-hybrid), MEIS1 (Two-hybrid), SP1 (Two-hybrid)
ESM2 similar proteins: A1YEY5, A1YFA5, A1YFI3, A1YG57, A2T733, A2T764, A2T7P4, A6NJ46, O42115, O43248, O43711, O55144, O95096, P02830, P09023, P09024, P09629, P09633, P17509, P17919, P18864, P23410, P28362, P29454, P31259, P31311, P31313, P31315, P42586, P43120, P43345, P43697, P48031, P52951, P53544, P53545, P53546, P56915, P97334, Q02591
Diamond homologs: A1YFT7, A2D5V0, A2D635, A2T6F8, A2T7D1, A2T7H7, B5DFK3, O42502, O42503, O42506, O43248, P09013, P09014, P09023, P09025, P09067, P09079, P09087, P09631, P09632, P09633, P10179, P14838, P15861, P17481, P17482, P17509, P18863, P18866, P20615, P23459, P23813, P24340, P24341, P24342, P28356, P28357, P28358, P28359, P31257
SIGNOR signaling
3 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| KDM6A | “up-regulates quantity by expression” | HOXC11 | “transcriptional regulation” |
| HOXC11 | “up-regulates quantity by expression” | S100B | “transcriptional regulation” |
| HOXC11 | up-regulates | HNF1A |
Disease & clinical
Clinical variants and AI predictions
ClinVar
10 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 9 |
| Likely benign | 1 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
283 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 12:53973924:G:GG | donor_gain | 1.0000 |
| 12:53973912:G:GT | donor_gain | 0.9900 |
| 12:53973921:CCAG:C | donor_loss | 0.9900 |
| 12:53973923:AG:A | donor_loss | 0.9900 |
| 12:53973924:G:GA | donor_loss | 0.9900 |
| 12:53975157:ACTT:A | acceptor_gain | 0.9900 |
| 12:53975179:A:AG | acceptor_gain | 0.9900 |
| 12:53975180:G:GA | acceptor_gain | 0.9900 |
| 12:53975180:GAC:G | acceptor_gain | 0.9900 |
| 12:53973921:CCA:C | donor_gain | 0.9800 |
| 12:53973922:CA:C | donor_gain | 0.9800 |
| 12:53975157:A:AG | acceptor_gain | 0.9800 |
| 12:53975158:C:G | acceptor_gain | 0.9800 |
| 12:53975176:TCCAG:T | acceptor_loss | 0.9800 |
| 12:53975177:CCAG:C | acceptor_loss | 0.9800 |
| 12:53975178:CAGA:C | acceptor_loss | 0.9800 |
| 12:53975179:A:C | acceptor_loss | 0.9800 |
| 12:53975179:AGAC:A | acceptor_gain | 0.9800 |
| 12:53975180:GA:G | acceptor_gain | 0.9800 |
| 12:53975180:GACG:G | acceptor_gain | 0.9800 |
| 12:53975180:GACGC:G | acceptor_gain | 0.9800 |
| 12:53973920:CCCA:C | donor_gain | 0.9700 |
| 12:53975505:C:A | acceptor_gain | 0.9700 |
| 12:53973919:CCCCA:C | donor_gain | 0.9600 |
| 12:53974277:G:GT | donor_gain | 0.9400 |
| 12:53973760:C:T | donor_gain | 0.9300 |
| 12:53975160:T:TA | acceptor_gain | 0.9200 |
| 12:53975154:C:A | acceptor_gain | 0.8800 |
| 12:53973911:G:GT | donor_gain | 0.8500 |
| 12:53973848:G:GT | donor_gain | 0.8300 |
AlphaMissense
1965 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 12:53975204:C:A | R236S | 1.000 |
| 12:53975204:C:T | R236C | 1.000 |
| 12:53975213:T:C | Y239H | 1.000 |
| 12:53975213:T:G | Y239D | 1.000 |
| 12:53975214:A:G | Y239C | 1.000 |
| 12:53975227:G:C | Q243H | 1.000 |
| 12:53975227:G:T | Q243H | 1.000 |
| 12:53975229:T:G | I244S | 1.000 |
| 12:53975232:G:C | R245P | 1.000 |
| 12:53975238:T:A | L247Q | 1.000 |
| 12:53975238:T:C | L247P | 1.000 |
| 12:53975238:T:G | L247R | 1.000 |
| 12:53975240:G:A | E248K | 1.000 |
| 12:53975241:A:T | E248V | 1.000 |
| 12:53975242:G:C | E248D | 1.000 |
| 12:53975242:G:T | E248D | 1.000 |
| 12:53975244:G:C | R249P | 1.000 |
| 12:53975246:G:A | E250K | 1.000 |
| 12:53975249:T:A | F251I | 1.000 |
| 12:53975249:T:C | F251L | 1.000 |
| 12:53975249:T:G | F251V | 1.000 |
| 12:53975250:T:C | F251S | 1.000 |
| 12:53975250:T:G | F251C | 1.000 |
| 12:53975251:T:A | F251L | 1.000 |
| 12:53975251:T:G | F251L | 1.000 |
| 12:53975264:T:C | Y256H | 1.000 |
| 12:53975264:T:G | Y256D | 1.000 |
| 12:53975265:A:G | Y256C | 1.000 |
| 12:53975268:T:A | I257N | 1.000 |
| 12:53975268:T:C | I257T | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000921625 (12:53973330 C>T), RS1001373646 (12:53973910 A>G), RS1001538915 (12:53975582 T>A), RS1001888327 (12:53974126 G>T), RS1002759828 (12:53972982 C>A,G,T), RS1002783761 (12:53972562 G>T), RS1002859654 (12:53976821 T>A,C), RS1003216059 (12:53977145 C>A,T), RS1003374468 (12:53971348 G>GA), RS1003896859 (12:53971601 G>A,T), RS1004791199 (12:53977334 A>G), RS1006063441 (12:53972422 G>A), RS1006120679 (12:53972746 A>T), RS1006738783 (12:53974933 C>A,G,T), RS1007789162 (12:53973991 G>A,C)
Disease associations
OMIM: gene MIM:605559 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
5 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST005956_70 | Waist-to-hip ratio adjusted for BMI | 4.000000e-13 |
| GCST005957_6 | Waist-to-hip ratio adjusted for BMI (age <50) | 6.000000e-06 |
| GCST005958_9 | Waist-to-hip ratio adjusted for BMI (age >50) | 1.000000e-08 |
| GCST005962_20 | Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test) | 7.000000e-13 |
| GCST90014033_57 | Haemorrhoidal disease | 7.000000e-10 |
EFO canonical traits (3, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0007788 | BMI-adjusted waist-hip ratio |
| EFO:0008007 | age at assessment |
| EFO:0008343 | sex interaction measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
15 total (human), top 15 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Aflatoxin B1 | decreases methylation | 2 |
| arsenite | increases methylation | 1 |
| sodium arsenite | affects methylation | 1 |
| Grape Seed Proanthocyanidins | affects cotreatment, increases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| Benzo(a)pyrene | affects methylation | 1 |
| Catechin | increases expression, affects cotreatment | 1 |
| Estradiol | decreases expression | 1 |
| Fluorouracil | affects expression, affects response to substance | 1 |
| Methylcholanthrene | affects binding, increases reaction | 1 |
| Nickel | decreases expression | 1 |
| Asbestos, Serpentine | decreases methylation | 1 |
| Asbestos, Crocidolite | decreases methylation | 1 |
| Asbestos, Amosite | decreases methylation | 1 |
| Lactic Acid | increases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): hemorrhoid