SUCO
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Also known as CH1SLP1OPT
Summary
SUCO (SUN domain containing ossification factor, HGNC:1240) is a protein-coding gene on chromosome 1q24.3, encoding SUN domain-containing ossification factor (Q9UBS9). Required for bone modeling during late embryogenesis.
Predicted to be involved in positive regulation of collagen biosynthetic process; positive regulation of osteoblast differentiation; and regulation of bone remodeling. Predicted to be located in rough endoplasmic reticulum. Predicted to be active in cytoplasm and membrane.
Source: NCBI Gene 51430 — RefSeq curated summary.
At a glance
- Gene–disease (curated): osteogenesis imperfecta (Moderate, GenCC) — +1 more curated relationship
- GWAS associations: 3
- Clinical variants (ClinVar): 565 total
- MANE Select transcript:
NM_014283
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:1240 |
| Approved symbol | SUCO |
| Name | SUN domain containing ossification factor |
| Location | 1q24.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | CH1, SLP1, OPT |
| Ensembl gene | ENSG00000094975 |
| Ensembl biotype | protein_coding |
| OMIM | 619434 |
| Entrez | 51430 |
Gene structure
Transcript identifiers
Ensembl transcripts: 9 — 5 retained_intron, 4 protein_coding
ENST00000263688, ENST00000367723, ENST00000486569, ENST00000608566, ENST00000608673, ENST00000608804, ENST00000609685, ENST00000610051, ENST00000616058
RefSeq mRNA: 4 — MANE Select: NM_014283
NM_001282750, NM_001282751, NM_014283, NM_016227
CCDS: CCDS1303, CCDS65726, CCDS65727, CCDS72984
Canonical transcript exons
ENST00000263688 — 24 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000451153 | 172608747 | 172608802 |
| ENSE00000610473 | 172573891 | 172573998 |
| ENSE00000789837 | 172553260 | 172553370 |
| ENSE00000789845 | 172569019 | 172569142 |
| ENSE00000789847 | 172570663 | 172570730 |
| ENSE00000789852 | 172578298 | 172578389 |
| ENSE00000789861 | 172602696 | 172602787 |
| ENSE00000814616 | 172555869 | 172556023 |
| ENSE00000814617 | 172557280 | 172557417 |
| ENSE00000814618 | 172557644 | 172557794 |
| ENSE00000814620 | 172570047 | 172570171 |
| ENSE00000814626 | 172579202 | 172579267 |
| ENSE00000814629 | 172588760 | 172589926 |
| ENSE00000814630 | 172590984 | 172591071 |
| ENSE00000814631 | 172600064 | 172600168 |
| ENSE00000814632 | 172602064 | 172602218 |
| ENSE00001068358 | 172585018 | 172585086 |
| ENSE00001068360 | 172551512 | 172551626 |
| ENSE00001068365 | 172585858 | 172585948 |
| ENSE00001068367 | 172575518 | 172575623 |
| ENSE00001068368 | 172577539 | 172577559 |
| ENSE00001068370 | 172577764 | 172577819 |
| ENSE00001906524 | 172533150 | 172533497 |
| ENSE00003719083 | 172609816 | 172611833 |
Expression profiles
Bgee: expression breadth ubiquitous, 297 present calls, max score 98.48.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.4571 / max 342.1206, expressed in 1783 samples.
FANTOM5 promoters (7 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 6696 | 12.9212 | 1752 |
| 6694 | 3.3316 | 1220 |
| 6695 | 1.3904 | 825 |
| 6697 | 0.3259 | 137 |
| 6698 | 0.1824 | 77 |
| 6693 | 0.1641 | 72 |
| 6700 | 0.1416 | 54 |
Top tissues by expression
299 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| corpus epididymis | UBERON:0004359 | 98.48 | gold quality |
| seminal vesicle | UBERON:0000998 | 96.80 | gold quality |
| jejunal mucosa | UBERON:0000399 | 96.59 | gold quality |
| germinal epithelium of ovary | UBERON:0001304 | 96.46 | gold quality |
| sperm | CL:0000019 | 95.72 | gold quality |
| parietal pleura | UBERON:0002400 | 95.38 | gold quality |
| bone marrow cell | CL:0002092 | 95.19 | gold quality |
| bone marrow | UBERON:0002371 | 95.17 | gold quality |
| male germ cell | CL:0000015 | 95.07 | gold quality |
| caput epididymis | UBERON:0004358 | 94.93 | gold quality |
| cauda epididymis | UBERON:0004360 | 94.46 | gold quality |
| hair follicle | UBERON:0002073 | 94.38 | gold quality |
| pleura | UBERON:0000977 | 93.89 | gold quality |
| oocyte | CL:0000023 | 93.75 | gold quality |
| calcaneal tendon | UBERON:0003701 | 93.51 | gold quality |
| palpebral conjunctiva | UBERON:0001812 | 93.49 | gold quality |
| ventricular zone | UBERON:0003053 | 93.28 | gold quality |
| tongue squamous epithelium | UBERON:0006919 | 93.26 | gold quality |
| islet of Langerhans | UBERON:0000006 | 93.23 | gold quality |
| tibia | UBERON:0000979 | 92.91 | gold quality |
| secondary oocyte | CL:0000655 | 92.68 | gold quality |
| pancreas | UBERON:0001264 | 92.42 | gold quality |
| cartilage tissue | UBERON:0002418 | 92.42 | gold quality |
| eye | UBERON:0000970 | 92.38 | gold quality |
| mucosa of paranasal sinus | UBERON:0005030 | 92.27 | gold quality |
| visceral pleura | UBERON:0002401 | 92.24 | gold quality |
| body of pancreas | UBERON:0001150 | 91.95 | gold quality |
| adrenal tissue | UBERON:0018303 | 91.76 | gold quality |
| lower lobe of lung | UBERON:0008949 | 91.53 | gold quality |
| embryo | UBERON:0000922 | 91.50 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 0.00 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
161 targeting SUCO, 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-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-340-5P | 100.00 | 72.50 | 4437 |
| HSA-MIR-513A-5P | 100.00 | 69.77 | 2465 |
| HSA-MIR-4747-5P | 100.00 | 67.90 | 2681 |
| HSA-MIR-5196-5P | 100.00 | 67.98 | 2761 |
| HSA-MIR-548AW | 99.99 | 72.57 | 3559 |
| HSA-MIR-196A-1-3P | 99.99 | 72.15 | 2772 |
| 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-12136 | 99.98 | 72.81 | 5713 |
| HSA-MIR-520D-5P | 99.98 | 73.34 | 4883 |
| HSA-MIR-524-5P | 99.98 | 73.43 | 4882 |
| HSA-MIR-607 | 99.97 | 73.62 | 5593 |
| HSA-MIR-3065-5P | 99.97 | 71.56 | 3281 |
| HSA-MIR-548AN | 99.97 | 70.91 | 2817 |
| HSA-MIR-5688 | 99.96 | 73.23 | 4504 |
| HSA-MIR-495-3P | 99.96 | 72.81 | 4197 |
| HSA-MIR-302E | 99.96 | 70.74 | 2669 |
| HSA-MIR-551B-5P | 99.96 | 71.28 | 3493 |
| HSA-MIR-128-3P | 99.95 | 71.17 | 2484 |
| HSA-MIR-216A-3P | 99.95 | 71.19 | 2505 |
| HSA-MIR-1236-3P | 99.94 | 68.04 | 1695 |
| HSA-MIR-497-5P | 99.92 | 71.83 | 2674 |
| HSA-MIR-145-5P | 99.92 | 71.13 | 1836 |
| HSA-MIR-5195-3P | 99.92 | 70.92 | 1877 |
| HSA-MIR-450B-5P | 99.92 | 71.48 | 3175 |
| HSA-MIR-7-1-3P | 99.91 | 71.53 | 4384 |
| HSA-MIR-7-2-3P | 99.91 | 71.40 | 4394 |
Literature-anchored findings (GeneRIF, showing 1)
- neurons have abnormal development due to lack of SUCO, which may be a generalized-onset epilepsy-related gene (PMID:25668491)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | suco | ENSDARG00000016532 |
| mus_musculus | Suco | ENSMUSG00000040297 |
| rattus_norvegicus | Suco | ENSRNOG00000026542 |
| drosophila_melanogaster | CG31678 | FBGN0051678 |
| caenorhabditis_elegans | suco-1 | WBGENE00020031 |
Protein
Protein identifiers
SUN domain-containing ossification factor — Q9UBS9 (reviewed: Q9UBS9)
Alternative names: Membrane protein CH1, Protein osteopotentia homolog, SUN-like protein 1
All UniProt accessions (3): Q9UBS9, A0A087WV04, B4DYM4
UniProt curated annotations — full annotation on UniProt →
Function. Required for bone modeling during late embryogenesis. Regulates type I collagen synthesis in osteoblasts during their postnatal maturation.
Subcellular location. Rough endoplasmic reticulum membrane.
Tissue specificity. Highly expressed in pancreas and testis and to a lower extent in prostate, ovary, heart, thymus, small intestine and spleen.
Post-translational modifications. O-glycosylated. O-mannosylated by POMT1 and POMT2 and elongated by POMGNT1. N-glycosylated.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q9UBS9-1 | 1 | yes |
| Q9UBS9-2 | 2 |
RefSeq proteins (4): NP_001269679, NP_001269680, NP_055098, NP_057311 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR008979 | Galactose-bd-like_sf | Homologous_superfamily |
| IPR012919 | SUN_dom | Domain |
| IPR045120 | Suco/Slp1-like | Family |
Pfam: PF07738
UniProt features (29 total): region of interest 7, compositionally biased region 6, glycosylation site 5, splice variant 3, sequence conflict 2, signal peptide 1, chain 1, coiled-coil region 1, modified residue 1, transmembrane region 1, domain 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9UBS9-F1 | 53.03 | 0.17 |
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): 1081
Glycosylation sites (5): 202, 236, 524, 928, 955
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 268 (showing top):
BROWNE_HCMV_INFECTION_30MIN_DN, GSE45365_NK_CELL_VS_BCELL_DN, GCACCTT_MIR18A_MIR18B, RRAGTTGT_UNKNOWN, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, CMYB_01, GOBP_OSTEOBLAST_DIFFERENTIATION, PATIL_LIVER_CANCER, GTGCCTT_MIR506, MARTINEZ_RB1_TARGETS_UP, MODULE_239, GOBP_POSITIVE_REGULATION_OF_CELL_DIFFERENTIATION, GOBP_REGULATION_OF_BONE_REMODELING, BOYAULT_LIVER_CANCER_SUBCLASS_G123_UP, HTF_01
GO Biological Process (4): ossification (GO:0001503), positive regulation of collagen biosynthetic process (GO:0032967), positive regulation of osteoblast differentiation (GO:0045669), regulation of bone remodeling (GO:0046850)
GO Molecular Function (0):
GO Cellular Component (5): cytoplasm (GO:0005737), rough endoplasmic reticulum (GO:0005791), membrane (GO:0016020), rough endoplasmic reticulum membrane (GO:0030867), endoplasmic reticulum (GO:0005783)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 2 |
| multicellular organismal process | 1 |
| positive regulation of biosynthetic process | 1 |
| positive regulation of collagen metabolic process | 1 |
| collagen biosynthetic process | 1 |
| regulation of collagen biosynthetic process | 1 |
| osteoblast differentiation | 1 |
| positive regulation of cell differentiation | 1 |
| regulation of osteoblast differentiation | 1 |
| regulation of tissue remodeling | 1 |
| bone remodeling | 1 |
| intracellular anatomical structure | 1 |
| endoplasmic reticulum | 1 |
| endoplasmic reticulum membrane | 1 |
| rough endoplasmic reticulum | 1 |
| bounding membrane of organelle | 1 |
| cytoplasm | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
Protein interactions and networks
STRING
1150 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| SUCO | MYL3 | P08590 | 890 |
| SUCO | HIF1A | Q16665 | 865 |
| SUCO | FCGRT | P55899 | 735 |
| SUCO | EP300 | Q09472 | 685 |
| SUCO | EPAS1 | Q99814 | 663 |
| SUCO | HSP90AA1 | P07900 | 651 |
| SUCO | AHSA1 | O95433 | 640 |
| SUCO | ARHGAP33 | O14559 | 618 |
| SUCO | CDR2 | Q01850 | 610 |
| SUCO | IGLL5 | B9A064 | 605 |
| SUCO | CITED2 | Q99967 | 593 |
| SUCO | IGHV4-38-2 | P0DP08 | 581 |
| SUCO | EIF5B | O60841 | 534 |
| SUCO | ACTN4 | O43707 | 530 |
| SUCO | DUSP1 | P28562 | 529 |
IntAct
31 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| P4HB | P4HA2 | psi-mi:“MI:0914”(association) | 0.740 |
| YWHAH | PLEKHG3 | psi-mi:“MI:0914”(association) | 0.610 |
| KCNS3 | UPK3BL1 | psi-mi:“MI:0914”(association) | 0.530 |
| P4HB | ZBTB2 | psi-mi:“MI:0914”(association) | 0.530 |
| YWHAQ | IGLC7 | psi-mi:“MI:0914”(association) | 0.530 |
| FBXO2 | TMEM131L | psi-mi:“MI:0914”(association) | 0.530 |
| TRAPPC1 | TRAPPC13 | psi-mi:“MI:0914”(association) | 0.530 |
| DNASE2B | ARSA | psi-mi:“MI:0914”(association) | 0.530 |
| SUCO | H4C16 | psi-mi:“MI:0915”(physical association) | 0.400 |
| Mis12 | psi-mi:“MI:0914”(association) | 0.350 | |
| Ptpn13 | CHPF2 | psi-mi:“MI:0914”(association) | 0.350 |
| Tapt1 | DERL1 | psi-mi:“MI:0914”(association) | 0.350 |
| SUCO | RPL10 | psi-mi:“MI:0914”(association) | 0.350 |
| TRAPPC1 | TRAPPC13 | psi-mi:“MI:0914”(association) | 0.350 |
| DNASE2B | psi-mi:“MI:0914”(association) | 0.350 | |
| YWHAB | PLEKHG3 | psi-mi:“MI:0914”(association) | 0.350 |
| YWHAG | C1orf226 | psi-mi:“MI:0914”(association) | 0.350 |
| YWHAZ | SPEG | psi-mi:“MI:0914”(association) | 0.350 |
| YWHAB | FOXO6 | psi-mi:“MI:0914”(association) | 0.350 |
| YWHAG | FOXO6 | psi-mi:“MI:0914”(association) | 0.350 |
| YWHAQ | FOXO6 | psi-mi:“MI:0914”(association) | 0.350 |
| YWHAH | FOXO6 | psi-mi:“MI:0914”(association) | 0.350 |
| TTMP | TMEM223 | psi-mi:“MI:0914”(association) | 0.350 |
| YWHAZ | HECTD4 | psi-mi:“MI:0914”(association) | 0.350 |
| CREB3L2 | PLEKHG3 | psi-mi:“MI:0914”(association) | 0.350 |
| SLC27A6 | NBAS | psi-mi:“MI:0914”(association) | 0.350 |
| PSTPIP1 | SUCO | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (83): SUCO (Affinity Capture-MS), SUCO (Affinity Capture-MS), CALU (Affinity Capture-MS), TNPO1 (Affinity Capture-MS), P4HB (Affinity Capture-MS), PREP (Affinity Capture-MS), PSMD11 (Affinity Capture-MS), RPL10 (Affinity Capture-MS), PHLDA2 (Affinity Capture-MS), MED24 (Affinity Capture-MS), NIPBL (Affinity Capture-MS), NDUFB11 (Affinity Capture-MS), SLC35F6 (Affinity Capture-MS), ELOVL5 (Affinity Capture-MS), GMCL1 (Affinity Capture-MS)
ESM2 similar proteins: A9QM73, B9DHD7, F4HP88, F4I316, F4I7C7, F4I8I0, F4JPE9, F4JRP0, F4JTI1, F4K1B1, F4K487, F4K4D6, M1BJF6, O04539, O48686, O48802, O65573, O81283, P0C8Q4, P48785, Q0D5P3, Q0WUR5, Q12232, Q710E6, Q8GZ87, Q8W4L5, Q940Y3, Q9C5S2, Q9FGT1, Q9FKV5, Q9FNE4, Q9FPT5, Q9LFQ3, Q9LFY0, Q9LNC4, Q9LUM0, Q9LUQ3, Q9LYE3, Q9M658, Q9MA60
Diamond homologs: F4I316, F4I8I0, F4JPE9, O59729, Q12232, Q54MI3, Q710E6, Q8C341, Q9UBS9
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 35 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.
Reactome pathways:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| Activation of BAD and translocation to mitochondria | 5 | 165.5× | 5e-09 |
| Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex | 5 | 146.0× | 6e-09 |
| SARS-CoV-1 targets host intracellular signalling and regulatory pathways | 5 | 146.0× | 6e-09 |
| Activation of BH3-only proteins | 5 | 107.9× | 3e-08 |
| RHO GTPases activate PKNs | 5 | 69.0× | 3e-07 |
| Intrinsic Pathway for Apoptosis | 5 | 63.7× | 3e-07 |
| SARS-CoV-1-host interactions | 5 | 38.2× | 4e-06 |
| Apoptosis | 5 | 36.5× | 4e-06 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| intracellular protein localization | 5 | 19.4× | 3e-04 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
565 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 347 |
| Likely benign | 175 |
| Benign | 19 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
3059 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 1:172533493:GTCTG:G | donor_gain | 1.0000 |
| 1:172533495:CTGG:C | donor_loss | 1.0000 |
| 1:172533496:TGGTG:T | donor_loss | 1.0000 |
| 1:172533498:G:GG | donor_gain | 1.0000 |
| 1:172533499:T:A | donor_loss | 1.0000 |
| 1:172551482:T:A | acceptor_gain | 1.0000 |
| 1:172551489:T:A | acceptor_gain | 1.0000 |
| 1:172551507:TACAG:T | acceptor_loss | 1.0000 |
| 1:172551509:CA:C | acceptor_loss | 1.0000 |
| 1:172551510:A:AG | acceptor_gain | 1.0000 |
| 1:172551510:AG:A | acceptor_gain | 1.0000 |
| 1:172551511:G:GA | acceptor_gain | 1.0000 |
| 1:172551511:GG:G | acceptor_gain | 1.0000 |
| 1:172551622:AAAAG:A | donor_loss | 1.0000 |
| 1:172551623:AAAG:A | donor_loss | 1.0000 |
| 1:172551624:AAGGT:A | donor_loss | 1.0000 |
| 1:172551625:AGGTG:A | donor_loss | 1.0000 |
| 1:172551626:GGTGC:G | donor_loss | 1.0000 |
| 1:172551627:G:T | donor_loss | 1.0000 |
| 1:172551628:T:G | donor_loss | 1.0000 |
| 1:172553371:G:GG | donor_gain | 1.0000 |
| 1:172553376:C:G | donor_gain | 1.0000 |
| 1:172555863:A:AG | acceptor_gain | 1.0000 |
| 1:172555867:A:AG | acceptor_gain | 1.0000 |
| 1:172555867:A:AT | acceptor_loss | 1.0000 |
| 1:172555868:G:GT | acceptor_gain | 1.0000 |
| 1:172555868:GA:G | acceptor_gain | 1.0000 |
| 1:172555868:GAA:G | acceptor_gain | 1.0000 |
| 1:172555868:GAAT:G | acceptor_gain | 1.0000 |
| 1:172555868:GAATA:G | acceptor_gain | 1.0000 |
AlphaMissense
8224 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 1:172569098:T:G | F271C | 1.000 |
| 1:172569106:T:A | W274R | 1.000 |
| 1:172569106:T:C | W274R | 1.000 |
| 1:172569108:G:C | W274C | 1.000 |
| 1:172569108:G:T | W274C | 1.000 |
| 1:172570122:C:A | A311D | 1.000 |
| 1:172570133:T:C | C315R | 1.000 |
| 1:172570135:T:G | C315W | 1.000 |
| 1:172570137:G:A | G316D | 1.000 |
| 1:172570140:C:A | A317D | 1.000 |
| 1:172570679:T:C | L333P | 1.000 |
| 1:172570715:G:A | C345Y | 1.000 |
| 1:172570716:C:G | C345W | 1.000 |
| 1:172573905:T:C | L355P | 1.000 |
| 1:172573907:T:C | C356R | 1.000 |
| 1:172573908:G:A | C356Y | 1.000 |
| 1:172573909:T:G | C356W | 1.000 |
| 1:172573955:T:C | F372L | 1.000 |
| 1:172573957:T:A | F372L | 1.000 |
| 1:172573957:T:G | F372L | 1.000 |
| 1:172573983:T:A | V381D | 1.000 |
| 1:172573991:A:C | S384R | 1.000 |
| 1:172573993:T:A | S384R | 1.000 |
| 1:172573993:T:G | S384R | 1.000 |
| 1:172575534:T:A | W392R | 1.000 |
| 1:172575534:T:C | W392R | 1.000 |
| 1:172575536:G:C | W392C | 1.000 |
| 1:172575536:G:T | W392C | 1.000 |
| 1:172577800:T:C | C441R | 1.000 |
| 1:172577801:G:A | C441Y | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000027110 (1:172535503 C>G), RS1000096698 (1:172588083 A>C,G), RS1000120342 (1:172540258 G>A), RS1000149093 (1:172605242 C>A), RS1000153355 (1:172568057 A>C), RS1000180563 (1:172605016 G>A,T), RS1000202675 (1:172530865 T>C), RS1000242796 (1:172548567 A>G), RS1000295027 (1:172548285 T>C), RS1000297003 (1:172592303 A>G), RS1000384572 (1:172597241 T>G), RS1000405115 (1:172611695 C>T), RS1000410418 (1:172580686 A>C), RS1000492298 (1:172561005 C>T), RS1000514883 (1:172588438 G>A,C)
Disease associations
OMIM: gene MIM:619434 | disease phenotypes:
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| osteogenesis imperfecta | Moderate | Autosomal recessive |
| temporal lobe epilepsy | Limited | Autosomal dominant |
Mondo (2): temporal lobe epilepsy (MONDO:0005115), osteogenesis imperfecta (MONDO:0019019)
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
3 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST003448_5 | Erythrocyte cadmium concentration in never smokers | 5.000000e-06 |
| GCST003518_51 | Daytime sleep phenotypes | 3.000000e-06 |
| GCST009391_1133 | Metabolite levels | 6.000000e-06 |
EFO canonical traits (2, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0007828 | daytime rest measurement |
| EFO:0010489 | glycerophosphocholine measurement |
MeSH disease descriptors (2)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D004833 | Epilepsy, Temporal Lobe | C10.228.140.490.360.290; C10.228.140.490.493.375 |
| D010013 | Osteogenesis Imperfecta | C05.116.099.708.685; C16.320.737; C17.300.200.540 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
29 total (human), top 29 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Cyclosporine | increases expression | 4 |
| Tretinoin | increases expression | 2 |
| GSK-J4 | increases expression | 1 |
| FR900359 | decreases phosphorylation | 1 |
| dicrotophos | decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | increases expression | 1 |
| sodium arsenite | increases expression | 1 |
| cobaltous chloride | increases expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| jinfukang | decreases expression | 1 |
| Sunitinib | increases expression | 1 |
| Leflunomide | increases expression | 1 |
| Acetaminophen | increases expression | 1 |
| Vehicle Emissions | increases abundance, increases expression | 1 |
| Cadmium | increases abundance, increases expression | 1 |
| Caffeine | affects phosphorylation | 1 |
| Carbamazepine | affects expression | 1 |
| Dimethyl Sulfoxide | decreases expression | 1 |
| Estradiol | increases expression | 1 |
| Thiram | increases expression | 1 |
| Tobacco Smoke Pollution | increases expression | 1 |
| Valproic Acid | decreases methylation, increases expression | 1 |
| Aflatoxin B1 | decreases methylation | 1 |
| Asbestos, Serpentine | decreases methylation | 1 |
| Cadmium Chloride | increases abundance, increases expression | 1 |
| Okadaic Acid | increases expression | 1 |
| Copper Sulfate | increases expression | 1 |
| Particulate Matter | increases abundance, increases expression | 1 |
Clinical trials (associated diseases)
98 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT00595699 | PHASE4 | COMPLETED | Escitalopram Treatment of Major Depression in Patients With Temporal Lobe Epilepsy |
| NCT00131469 | PHASE4 | COMPLETED | Study of Teriparatide (FORTEO) to Treat Adults With Osteogenesis Imperfecta |
| NCT00159419 | PHASE4 | COMPLETED | Bisphosphonate Therapy for Osteogenesis Imperfecta |
| NCT01713231 | PHASE4 | COMPLETED | Effect of High-Dose Vitamin D on Bone Density in Osteogenesis Imperfecta |
| NCT02303873 | PHASE4 | COMPLETED | Efficacy and Safety of Alendronate in Chinese Children or Adolescents With Osteogenesis Imperfecta |
| NCT03735537 | PHASE4 | COMPLETED | Treatment of Osteogenesis Imperfecta With Parathyroid Hormone and Zoledronic Acid |
| NCT04152551 | PHASE4 | RECRUITING | Effects of Bisphosphonates on OI-Related Hearing Loss |
| NCT00717431 | PHASE3 | TERMINATED | A Multicenter Study of Hippocampal Electrical Stimulation (HS, in Mesial Temporal Lobe Epilepsy |
| NCT00001305 | PHASE3 | COMPLETED | Growth Hormone Therapy in Osteogenesis Imperfecta |
| NCT00005901 | PHASE3 | COMPLETED | Pamidronate to Treat Osteogenesis Imperfecta in Children |
| NCT00106028 | PHASE3 | COMPLETED | Safety and Efficacy of Risedronate in the Treatment of Osteogenesis Imperfecta in Children |
| NCT00982124 | PHASE3 | COMPLETED | An Efficacy and Safety Trial of Intravenous Zoledronic Acid in Infants Less Than One Year of Age, With Severe Osteogenesis Imperfecta |
| NCT02352753 | PHASE3 | TERMINATED | Multicenter,Single-arm Study to Evaluate Efficacy, Safety, & Pharmacokinetics of Denosumab in Children w/ OI |
| NCT03638128 | PHASE3 | TERMINATED | Open-label Extension of Study 20130173 of Denosumab in Children and Young Adults With Osteogenesis Imperfecta |
| NCT05768854 | PHASE3 | ACTIVE_NOT_RECRUITING | Setrusumab vs Bisphosphonates in Pediatric Subjects With Osteogenesis Imperfecta |
| NCT05972551 | PHASE3 | ACTIVE_NOT_RECRUITING | Study to Evaluate Efficacy and Safety of Romosozumab Compared With Bisphosphonates in Children and Adolescents With Osteogenesis Imperfecta |
| NCT06636071 | PHASE3 | ACTIVE_NOT_RECRUITING | Setrusumab in Pediatric Japanese Subjects With Osteogenesis Imperfecta |
| NCT07366086 | PHASE3 | RECRUITING | Pediatric Safety Follow-up Study of Prior Treatment With Romosozumab for Osteogenesis Imperfecta |
| NCT00063479 | PHASE2 | COMPLETED | Bisphosphonate Treatment of Osteogenesis Imperfecta |
| NCT00131118 | PHASE2 | COMPLETED | Zoledronic Acid in Children (1 -17 Years) With Severe Osteogenesis Imperfecta |
| NCT01417091 | PHASE2 | COMPLETED | Safety, Pharmacokinetics and Pharmacodynamics of BPS804 in Osteogenesis Imperfecta |
| NCT01679080 | PHASE2 | TERMINATED | The Effect of Treatment With Teriparatide and Zoledronic Acid in Patients With Osteogenesis Imperfecta |
| NCT01799798 | PHASE2 | COMPLETED | Translational Therapy in Patients With Osteogenesis Imperfecta - A Pilot Trial on Treatment With the Rankl-Antibody Denosumab |
| NCT03208582 | PHASE2 | COMPLETED | Do Bisphosphonates Alter the Skeletal Response to Mechanical Stimulation in Children With Osteogenesis Imperfecta? |
| NCT03216486 | PHASE2 | WITHDRAWN | An Exploratory Study of BPS804 Treatment in Adult Patients With Type I, III or IV Osteogenesis Imperfecta |
| NCT05312697 | PHASE2 | TERMINATED | Long-term Extension Study of Setrusumab in Adults With Type I, III, or IV Osteogenesis Imperfecta |
| NCT07062588 | PHASE2 | RECRUITING | Osteogenesis Imperfecta Trial of AGA2115 for ADUlts With COL1A1 and/or COL1A2 GeNetic Variations (IDUN) |
| NCT07557446 | PHASE2 | NOT_YET_RECRUITING | A Dose REgimen-Finding Study of AGA2115 in Chinese Patients With Osteogenesis ImpeRfecta (EIR) |
| NCT05179083 | PHASE1 | UNKNOWN | Exercise for Brain Regeneration in Epilepsy |
| NCT00705120 | PHASE1 | COMPLETED | Treatment of Severe Osteogenesis Imperfecta by Allogeneic Bone Marrow Transplantation |
| NCT02172885 | PHASE1 | COMPLETED | Mesenchymal Stem Cell Based Therapy for the Treatment of Osteogenesis Imperfecta |
| NCT03064074 | PHASE1 | COMPLETED | Safety of Fresolimumab in the Treatment of Osteogenesis Imperfecta |
| NCT04545554 | PHASE1 | COMPLETED | Study to Evaluate Romosozumab in Children and Adolescents With Osteogenesis Imperfecta |
| NCT05231668 | PHASE1 | TERMINATED | Single Ascending Dose Study of SAR439459 in Adults With Osteogenesis Imperfecta (OI) |
| NCT06086613 | PHASE1 | COMPLETED | A First-in-Human Study Evaluating AGA2115 in Adult Healthy Volunteers |
| NCT00344877 | Not specified | COMPLETED | Electrical Brain Stimulation to Reduce Epileptic Seizures |
| NCT02590419 | Not specified | UNKNOWN | Application of Diffusion Tensor Imaging and Tractography in Epilepsy Surgery |
| NCT02844465 | Not specified | COMPLETED | Stereotactic Laser Ablation for Temporal Lobe Epilepsy (Slate) |
| NCT02946151 | Not specified | COMPLETED | Subcutaneous EEG in Epilepsy |
| NCT03643471 | Not specified | UNKNOWN | Advanced Magnetic Resonance Imaging in Temporal Lobe Epilepsy |
Related Atlas pages
- Associated diseases: temporal lobe epilepsy, osteogenesis imperfecta
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): osteogenesis imperfecta, temporal lobe epilepsy