FAM20B
gene geneOn this page
Also known as KIAA0475GXK1
Summary
FAM20B (FAM20B glycosaminoglycan xylosylkinase, HGNC:23017) is a protein-coding gene on chromosome 1q25.2, encoding Glycosaminoglycan xylosylkinase (O75063). Responsible for the 2-O-phosphorylation of xylose in the glycosaminoglycan-protein linkage region of proteoglycans thereby regulating the amount of mature GAG chains.
Enables phosphotransferase activity, alcohol group as acceptor. Predicted to be involved in proteoglycan biosynthetic process. Located in Golgi apparatus and nucleoplasm.
Source: NCBI Gene 9917 — RefSeq curated summary.
At a glance
- Gene–disease (curated): Desbuquois dysplasia (Moderate, GenCC) — +1 more curated relationship
- GWAS associations: 1
- Clinical variants (ClinVar): 65 total
- MANE Select transcript:
NM_014864
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:23017 |
| Approved symbol | FAM20B |
| Name | FAM20B glycosaminoglycan xylosylkinase |
| Location | 1q25.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | KIAA0475, GXK1 |
| Ensembl gene | ENSG00000116199 |
| Ensembl biotype | protein_coding |
| OMIM | 611063 |
| Entrez | 9917 |
Gene structure
Transcript identifiers
Ensembl transcripts: 5 — 5 protein_coding
ENST00000263733, ENST00000440702, ENST00000889611, ENST00000929138, ENST00000957692
RefSeq mRNA: 3 — MANE Select: NM_014864
NM_001324310, NM_001324311, NM_014864
CCDS: CCDS1328
Canonical transcript exons
ENST00000263733 — 8 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000790070 | 179054529 | 179054638 |
| ENSE00000922003 | 179050279 | 179050365 |
| ENSE00001067519 | 179043715 | 179044224 |
| ENSE00001338868 | 179071913 | 179076567 |
| ENSE00001338869 | 179066800 | 179066859 |
| ENSE00001338870 | 179064305 | 179064496 |
| ENSE00001338872 | 179063927 | 179064098 |
| ENSE00001346787 | 179025894 | 179026098 |
Expression profiles
Bgee: expression breadth ubiquitous, 294 present calls, max score 94.60.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.1633 / max 275.0111, expressed in 1791 samples.
FANTOM5 promoters (3 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 6896 | 9.3425 | 1776 |
| 6895 | 0.9684 | 679 |
| 6897 | 0.8524 | 533 |
Top tissues by expression
302 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| lateral nuclear group of thalamus | UBERON:0002736 | 94.60 | gold quality |
| Brodmann (1909) area 10 | UBERON:0013541 | 93.84 | gold quality |
| saphenous vein | UBERON:0007318 | 93.17 | gold quality |
| lateral globus pallidus | UBERON:0002476 | 93.00 | gold quality |
| substantia nigra pars compacta | UBERON:0001965 | 92.87 | gold quality |
| substantia nigra pars reticulata | UBERON:0001966 | 92.50 | gold quality |
| adrenal tissue | UBERON:0018303 | 92.45 | gold quality |
| frontal pole | UBERON:0002795 | 92.36 | gold quality |
| dorsal root ganglion | UBERON:0000044 | 92.18 | gold quality |
| cauda epididymis | UBERON:0004360 | 91.83 | gold quality |
| trigeminal ganglion | UBERON:0001675 | 91.48 | gold quality |
| pericardium | UBERON:0002407 | 91.18 | gold quality |
| caput epididymis | UBERON:0004358 | 90.97 | gold quality |
| blood vessel layer | UBERON:0004797 | 90.95 | gold quality |
| skeletal muscle tissue of rectus abdominis | UBERON:0004511 | 90.86 | gold quality |
| corpus epididymis | UBERON:0004359 | 90.75 | gold quality |
| urethra | UBERON:0000057 | 90.39 | gold quality |
| popliteal artery | UBERON:0002250 | 90.22 | gold quality |
| tibial artery | UBERON:0007610 | 90.20 | gold quality |
| cerebellar vermis | UBERON:0004720 | 90.17 | gold quality |
| islet of Langerhans | UBERON:0000006 | 90.03 | gold quality |
| cortical plate | UBERON:0005343 | 90.01 | gold quality |
| parietal lobe | UBERON:0001872 | 89.94 | gold quality |
| superior vestibular nucleus | UBERON:0007227 | 89.85 | gold quality |
| olfactory bulb | UBERON:0002264 | 89.84 | gold quality |
| synovial joint | UBERON:0002217 | 89.82 | gold quality |
| middle frontal gyrus | UBERON:0002702 | 89.65 | gold quality |
| postcentral gyrus | UBERON:0002581 | 89.48 | gold quality |
| vena cava | UBERON:0004087 | 89.45 | gold quality |
| paraflocculus | UBERON:0005351 | 89.39 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 3.79 |
| E-MTAB-6379 | no | 66.31 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
178 targeting FAM20B, 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-4747-5P | 100.00 | 67.90 | 2681 |
| HSA-MIR-5196-5P | 100.00 | 67.98 | 2761 |
| HSA-MIR-5193 | 100.00 | 67.26 | 1744 |
| HSA-MIR-4668-3P | 100.00 | 68.74 | 2635 |
| HSA-MIR-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-7110-3P | 100.00 | 73.18 | 2486 |
| HSA-MIR-513A-5P | 100.00 | 69.77 | 2465 |
| HSA-MIR-6833-3P | 100.00 | 70.63 | 3197 |
| HSA-MIR-4768-5P | 100.00 | 69.49 | 2861 |
| HSA-MIR-3120-5P | 100.00 | 65.56 | 965 |
| HSA-MIR-9-5P | 100.00 | 72.28 | 2361 |
| HSA-MIR-371B-5P | 99.99 | 75.34 | 4759 |
| HSA-MIR-3662 | 99.99 | 73.82 | 5684 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-513B-5P | 99.99 | 69.96 | 2150 |
| HSA-MIR-12121 | 99.99 | 66.64 | 255 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-373-5P | 99.98 | 75.36 | 4753 |
| HSA-MIR-616-5P | 99.98 | 75.58 | 4775 |
| HSA-MIR-19A-3P | 99.98 | 75.33 | 2762 |
| HSA-MIR-19B-3P | 99.98 | 75.44 | 2754 |
| HSA-MIR-4789-5P | 99.98 | 70.76 | 2721 |
| HSA-MIR-5696 | 99.98 | 72.36 | 4487 |
| HSA-MIR-3692-3P | 99.98 | 70.27 | 2139 |
| HSA-MIR-6888-3P | 99.97 | 65.95 | 1170 |
| HSA-MIR-1250-3P | 99.96 | 70.04 | 4038 |
| HSA-LET-7C-3P | 99.95 | 73.42 | 2862 |
| HSA-MIR-1236-3P | 99.94 | 68.04 | 1695 |
| HSA-MIR-335-3P | 99.93 | 73.36 | 4958 |
| HSA-MIR-218-5P | 99.93 | 72.22 | 2103 |
Literature-anchored findings (GeneRIF, showing 2)
- The T allele of FAM20B (rs3766626) was associated with susceptibility to two mesiodens (PMID:31133012)
- Altered Expression of Aggrecan, FAM20B, B3GALT6, and EXTL2 in Patients with Osteoarthritis and Kashin-Beck Disease. (PMID:32517548)
Cross-species orthologs
4 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | fam20b | ENSDARG00000008573 |
| mus_musculus | Fam20b | ENSMUSG00000033557 |
| rattus_norvegicus | Fam20b | ENSRNOG00000004337 |
| drosophila_melanogaster | CG3631 | FBGN0038268 |
Paralogs (2): FAM20A (ENSG00000108950), FAM20C (ENSG00000177706)
Protein
Protein identifiers
Glycosaminoglycan xylosylkinase — O75063 (reviewed: O75063)
Alternative names: Xylose kinase
All UniProt accessions (2): O75063, X6RH03
UniProt curated annotations — full annotation on UniProt →
Function. Responsible for the 2-O-phosphorylation of xylose in the glycosaminoglycan-protein linkage region of proteoglycans thereby regulating the amount of mature GAG chains. Sulfated glycosaminoglycans (GAGs), including heparan sulfate and chondroitin sulfate, are synthesized on the so-called common GAG-protein linkage region (GlcUAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1-O-Ser) of core proteins, which is formed by the stepwise addition of monosaccharide residues by the respective specific glycosyltransferases. Xylose 2-O-phosphorylation may influence the catalytic activity of B3GAT3 (GlcAT-I) which completes the precursor tetrasaccharide of GAG-protein linkage regions on which the repeating disaccharide region is synthesized.
Subcellular location. Golgi apparatus membrane.
Tissue specificity. Widely expressed. Strongly expressed in pancreas, spleen and fetal liver.
Similarity. Belongs to the FAM20 family.
RefSeq proteins (3): NP_001311239, NP_001311240, NP_055679* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR009581 | FAM20_C | Domain |
| IPR024869 | FAM20 | Family |
Pfam: PF06702
Catalyzed reactions (Rhea), 1 shown:
- 3-O-(beta-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-xylosyl)-L-seryl-[protein] + ATP = 3-O-(beta-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-2-O-phosphoxylosyl)-L-seryl-[protein] + ADP + H(+) (RHEA:19461)
UniProt features (17 total): binding site 7, disulfide bond 4, topological domain 2, chain 1, glycosylation site 1, transmembrane region 1, active site 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-O75063-F1 | 93.14 | 0.84 |
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): 289
Ligand- & substrate-binding residues (7): 309; 309; 107; 123; 142; 222–225; 294
Disulfide bonds (4): 196–211, 201–204, 257–331, 332–389
Glycosylation sites (1): 193
Function
Pathways and Gene Ontology
Reactome pathways
1 pathways
| ID | Pathway |
|---|---|
| R-HSA-1971475 | Glycosaminoglycan-protein linkage region biosynthesis |
MSigDB gene sets: 152 (showing top):
MORF_MBD4, MORF_RAD21, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, MITSIADES_RESPONSE_TO_APLIDIN_DN, MORF_PSMC2, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_REGULATION_OF_GLYCOPROTEIN_METABOLIC_PROCESS, MORF_ATOX1, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, AACTTT_UNKNOWN, IK2_01, TAATGTG_MIR323, GOBP_GLYCOPROTEIN_METABOLIC_PROCESS, REACTOME_METABOLISM_OF_CARBOHYDRATES_AND_CARBOHYDRATE_DERIVATIVES
GO Biological Process (2): proteoglycan biosynthetic process (GO:0030166), negative regulation of proteoglycan biosynthetic process (GO:1902729)
GO Molecular Function (7): ATP binding (GO:0005524), kinase activity (GO:0016301), phosphotransferase activity, alcohol group as acceptor (GO:0016773), metal ion binding (GO:0046872), nucleotide binding (GO:0000166), protein binding (GO:0005515), transferase activity (GO:0016740)
GO Cellular Component (5): Golgi membrane (GO:0000139), nucleoplasm (GO:0005654), Golgi apparatus (GO:0005794), cytoplasm (GO:0005737), membrane (GO:0016020)
Reactome top-level categories
Rollup of top-1 pathways:
| Category | Pathways |
|---|---|
| Glycosaminoglycan metabolism | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 3 |
| transferase activity, transferring phosphorus-containing groups | 2 |
| proteoglycan metabolic process | 1 |
| glycoprotein biosynthetic process | 1 |
| negative regulation of glycoprotein biosynthetic process | 1 |
| proteoglycan biosynthetic process | 1 |
| adenyl ribonucleotide binding | 1 |
| purine ribonucleoside triphosphate binding | 1 |
| cation binding | 1 |
| nucleoside phosphate binding | 1 |
| heterocyclic compound binding | 1 |
| binding | 1 |
| catalytic activity | 1 |
| Golgi apparatus | 1 |
| bounding membrane of organelle | 1 |
| nuclear lumen | 1 |
| cytoplasm | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
| intracellular anatomical structure | 1 |
Protein interactions and networks
STRING
734 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| FAM20B | XYLT1 | Q86Y38 | 751 |
| FAM20B | GASK1A | Q9UFP1 | 714 |
| FAM20B | EXTL2 | Q9UBQ6 | 702 |
| FAM20B | B3GALT6 | Q96L58 | 699 |
| FAM20B | B3GAT3 | O94766 | 688 |
| FAM20B | B4GALT7 | Q9UBV7 | 672 |
| FAM20B | PXYLP1 | Q8TE99 | 669 |
| FAM20B | XYLT2 | Q9H1B5 | 657 |
| FAM20B | UXS1 | Q8NBZ7 | 653 |
| FAM20B | FJX1 | Q86VR8 | 645 |
| FAM20B | EXTL3 | O43909 | 604 |
| FAM20B | POMK | Q9H5K3 | 555 |
| FAM20B | EXT2 | Q93063 | 546 |
| FAM20B | CSGALNACT2 | Q8N6G5 | 537 |
| FAM20B | ENAM | Q9NRM1 | 529 |
IntAct
123 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| FAM20B | ASPHD2 | psi-mi:“MI:0915”(physical association) | 0.670 |
| FAM20B | ASPHD2 | psi-mi:“MI:0914”(association) | 0.670 |
| P2RX4 | FAM20B | psi-mi:“MI:0914”(association) | 0.640 |
| CD27 | TCAF2 | psi-mi:“MI:0914”(association) | 0.640 |
| FAM20B | DCN | psi-mi:“MI:0217”(phosphorylation reaction) | 0.620 |
| DCN | FAM20B | psi-mi:“MI:0217”(phosphorylation reaction) | 0.620 |
| FAM20B | KCNJ6 | psi-mi:“MI:0915”(physical association) | 0.560 |
| FFAR2 | FAM20B | psi-mi:“MI:0915”(physical association) | 0.560 |
| FAM20B | FAM209A | psi-mi:“MI:0915”(physical association) | 0.560 |
| FAM20B | GPR152 | psi-mi:“MI:0915”(physical association) | 0.560 |
| BSCL2 | FAM20B | psi-mi:“MI:0915”(physical association) | 0.560 |
| FAM20B | TIMMDC1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| FAM20B | SLC7A14 | psi-mi:“MI:0915”(physical association) | 0.560 |
| FAM20B | TMEM80 | psi-mi:“MI:0915”(physical association) | 0.560 |
| LPAR1 | TMEM223 | psi-mi:“MI:0914”(association) | 0.530 |
| IPPK | TMEM223 | psi-mi:“MI:0914”(association) | 0.530 |
| SPPL2B | UQCRQ | psi-mi:“MI:0914”(association) | 0.530 |
| SCN3B | ABCC5 | psi-mi:“MI:0914”(association) | 0.530 |
| GALNT6 | NDUFS4 | psi-mi:“MI:0914”(association) | 0.530 |
| PEX19 | FAM20B | psi-mi:“MI:0914”(association) | 0.530 |
| CENPH | PSMD11 | psi-mi:“MI:0914”(association) | 0.530 |
| PBXIP1 | GOLIM4 | psi-mi:“MI:0914”(association) | 0.530 |
| FAM174A | BLTP3B | psi-mi:“MI:0914”(association) | 0.530 |
BioGRID (103): FAM20B (Affinity Capture-MS), FAM20B (Affinity Capture-MS), FAM20B (Affinity Capture-MS), FAM20B (Affinity Capture-MS), FAM20B (Affinity Capture-MS), FAM20B (Affinity Capture-MS), FAM20B (Affinity Capture-MS), FAM20B (Affinity Capture-MS), FAM20B (Affinity Capture-MS), ASPHD2 (Affinity Capture-MS), FAM20B (Affinity Capture-MS), FAM20B (Affinity Capture-MS), FAM20B (Affinity Capture-MS), FAM20B (Affinity Capture-MS), FAM20B (Affinity Capture-MS)
ESM2 similar proteins: A2XFP3, A2ZI32, A4VCL2, B4JW99, B4LCX4, B8AIZ4, F4J2C8, O22775, O75063, O75072, P14599, P45895, P54360, P86275, Q0KHV6, Q10MQ0, Q2QXP0, Q2TBE6, Q5K027, Q5MJS3, Q5RH51, Q5SP46, Q5XIL2, Q5ZEQ8, Q5ZIK0, Q6DCQ8, Q6GX83, Q6H765, Q6PE18, Q701R1, Q701R2, Q86BJ3, Q8CBQ5, Q8CID3, Q8IXL6, Q8R507, Q8RXE1, Q8T5G8, Q8VCS3, Q93ZX7
Diamond homologs: A4VCL2, O75063, Q5MJS3, Q5RH51, Q8CID3, Q8IXL6, Q8VCS3, Q95T10, Q96MK3, Q9XTW2
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 114 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 |
|---|---|---|---|
| Glycosaminoglycan-protein linkage region biosynthesis | 5 | 25.9× | 3e-04 |
| Glycosaminoglycan metabolism | 6 | 17.3× | 3e-04 |
| R-HSA-425366 | 5 | 11.9× | 3e-03 |
| Metabolism of carbohydrates and carbohydrate derivatives | 6 | 9.5× | 2e-03 |
| SLC-mediated transmembrane transport | 8 | 6.2× | 2e-03 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| zinc ion transmembrane transport | 5 | 35.5× | 2e-04 |
| intracellular zinc ion homeostasis | 5 | 24.3× | 7e-04 |
| amino acid transport | 5 | 15.8× | 4e-03 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
65 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 52 |
| Likely benign | 1 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2402 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 1:179044222:GCG:G | donor_gain | 1.0000 |
| 1:179054514:A:AG | acceptor_gain | 1.0000 |
| 1:179057813:GGGC:G | donor_gain | 1.0000 |
| 1:179064302:CAGG:C | acceptor_loss | 1.0000 |
| 1:179064303:AGGTG:A | acceptor_gain | 1.0000 |
| 1:179064304:GGTGG:G | acceptor_gain | 1.0000 |
| 1:179064495:AGGTG:A | donor_loss | 1.0000 |
| 1:179064497:GT:G | donor_loss | 1.0000 |
| 1:179072113:TGG:T | donor_gain | 1.0000 |
| 1:179072115:G:GT | donor_gain | 1.0000 |
| 1:179072123:G:GT | donor_gain | 1.0000 |
| 1:179026096:CAGGT:C | donor_loss | 0.9900 |
| 1:179026097:AGGTG:A | donor_loss | 0.9900 |
| 1:179026100:T:A | donor_loss | 0.9900 |
| 1:179044223:CGGT:C | donor_loss | 0.9900 |
| 1:179044224:GGTAA:G | donor_loss | 0.9900 |
| 1:179044225:G:GG | donor_gain | 0.9900 |
| 1:179044225:GT:G | donor_loss | 0.9900 |
| 1:179044226:T:G | donor_loss | 0.9900 |
| 1:179050273:TTGCA:T | acceptor_loss | 0.9900 |
| 1:179050274:TGCA:T | acceptor_loss | 0.9900 |
| 1:179050275:GCA:G | acceptor_loss | 0.9900 |
| 1:179050276:CAG:C | acceptor_loss | 0.9900 |
| 1:179050277:A:AC | acceptor_loss | 0.9900 |
| 1:179050345:AGC:A | donor_gain | 0.9900 |
| 1:179050362:ACAG:A | donor_loss | 0.9900 |
| 1:179050364:AGGT:A | donor_loss | 0.9900 |
| 1:179050365:GG:G | donor_loss | 0.9900 |
| 1:179050367:T:A | donor_loss | 0.9900 |
| 1:179051282:GCCA:G | donor_gain | 0.9900 |
AlphaMissense
2674 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 1:179044160:G:A | G105R | 1.000 |
| 1:179044160:G:C | G105R | 1.000 |
| 1:179044161:G:A | G105E | 1.000 |
| 1:179044168:G:C | Q107H | 1.000 |
| 1:179044168:G:T | Q107H | 1.000 |
| 1:179044172:A:G | K109E | 1.000 |
| 1:179044173:A:T | K109I | 1.000 |
| 1:179044174:A:C | K109N | 1.000 |
| 1:179044174:A:T | K109N | 1.000 |
| 1:179044214:A:G | K123E | 1.000 |
| 1:179044216:A:C | K123N | 1.000 |
| 1:179044216:A:T | K123N | 1.000 |
| 1:179050326:A:T | D142V | 1.000 |
| 1:179050329:G:C | R143T | 1.000 |
| 1:179063940:T:G | C196W | 1.000 |
| 1:179063947:G:T | G199W | 1.000 |
| 1:179063948:G:A | G199E | 1.000 |
| 1:179063948:G:T | G199V | 1.000 |
| 1:179063953:T:A | C201S | 1.000 |
| 1:179063953:T:C | C201R | 1.000 |
| 1:179063954:G:A | C201Y | 1.000 |
| 1:179063954:G:C | C201S | 1.000 |
| 1:179063954:G:T | C201F | 1.000 |
| 1:179063955:C:G | C201W | 1.000 |
| 1:179063962:T:A | C204S | 1.000 |
| 1:179063962:T:C | C204R | 1.000 |
| 1:179063963:G:A | C204Y | 1.000 |
| 1:179063963:G:C | C204S | 1.000 |
| 1:179063963:G:T | C204F | 1.000 |
| 1:179063964:C:G | C204W | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000005619 (1:179035749 A>G), RS1000094800 (1:179047724 A>T), RS1000102718 (1:179067556 A>G), RS1000144334 (1:179015634 T>C), RS1000146420 (1:179057906 T>C), RS1000191186 (1:179015526 C>T), RS1000257251 (1:179051496 G>A,T), RS1000290524 (1:179055393 C>A,T), RS1000333621 (1:179042281 C>T), RS1000406585 (1:179045039 C>T), RS1000442365 (1:179048537 C>T), RS1000497440 (1:179057587 C>G), RS1000537545 (1:179052824 T>G), RS1000538881 (1:179074847 C>T), RS1000596112 (1:179075084 C>T)
Disease associations
OMIM: gene MIM:611063 | disease phenotypes:
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| Desbuquois dysplasia | Moderate | Autosomal recessive |
| congenital disorder of glycosylation | Limited | Autosomal recessive |
ClinGen Gene-Disease Validity (1)
Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.
| Disease | Classification | Inheritance |
|---|---|---|
| congenital disorder of glycosylation | Limited | AR |
Mondo (2): congenital disorder of glycosylation (MONDO:0015286), Desbuquois dysplasia (MONDO:0015426)
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
1 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST011426_3 | Systemic lupus erythematosus | 1.000000e-06 |
MeSH disease descriptors (1)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D018981 | Congenital Disorders of Glycosylation | C16.320.565.202.125; C18.452.648.202.125 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
20 total (human), top 20 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Cadmium Chloride | increases expression, increases methylation | 2 |
| aristolochic acid I | decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| arsenite | affects binding, decreases reaction | 1 |
| butyraldehyde | decreases expression | 1 |
| perfluorooctanoic acid | decreases expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| CGP 52608 | increases reaction, affects binding | 1 |
| abrine | decreases expression | 1 |
| Bortezomib | decreases expression | 1 |
| Temozolomide | decreases expression | 1 |
| Benzo(a)pyrene | affects methylation, increases methylation | 1 |
| Doxorubicin | decreases expression | 1 |
| Formaldehyde | decreases expression | 1 |
| Methyl Methanesulfonate | decreases expression | 1 |
| Tretinoin | decreases expression | 1 |
| Tunicamycin | decreases expression | 1 |
| Valproic Acid | decreases expression | 1 |
| 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide | decreases expression | 1 |
| Aflatoxin B1 | decreases methylation | 1 |
Cellosaurus cell lines
5 cell lines: 5 cancer cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_B1RU | Abcam HeLa FAM20B KO | Cancer cell line | Female |
| CVCL_DX00 | HAP1 FAM20B (-) 2 | Cancer cell line | Male |
| CVCL_DX33 | HAP1 FAM20B (-) IDS (-) 1 | Cancer cell line | Male |
| CVCL_DX34 | HAP1 FAM20B (-) IDS (-) 2 | Cancer cell line | Male |
| CVCL_XN67 | HAP1 FAM20B (-) 1 | Cancer cell line | Male |
Clinical trials (associated diseases)
9 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT07572825 | PHASE1 | NOT_YET_RECRUITING | Assessing the Safety and Tolerability of NMN in DHDDS-CDG |
| NCT02089789 | Not specified | RECRUITING | Clinical and Basic Investigations Into Known and Suspected Congenital Disorders of Glycosylation |
| NCT02503267 | Not specified | UNKNOWN | Incidence and Consequences of Disorders of Glycosylation in Patients With Conotruncal and Septal Heart Defects |
| NCT02955264 | Not specified | COMPLETED | Using D-Galactose as a Food Supplement in Congenital Disorders of Glycosylation |
| NCT03250728 | Not specified | COMPLETED | Role of the Endothelium in Stroke-like Episode Among CDG Patients |
| NCT03560570 | Not specified | COMPLETED | Study of Hemostasis in Patients With Congenital Disorder of Glycosylation |
| NCT04198987 | Not specified | COMPLETED | Dietary Monosaccharide Supplementation in Patients With Congenital Disorders of Glycosylation |
| NCT04199000 | Not specified | RECRUITING | Clinical and Basic Investigations Into Congenital Disorders of Glycosylation |
| NCT04201067 | Not specified | COMPLETED | Large-Scale Metabolomic Profiling for the Diagnosis of Inborn Errors of Metabolism |
Related Atlas pages
- Associated diseases: congenital disorder of glycosylation, Desbuquois dysplasia
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): congenital disorder of glycosylation, Desbuquois dysplasia