SUPT20H

Summary

SUPT20H (SPT20 homolog, SAGA complex component, HGNC:20596) is a protein-coding gene on chromosome 13q13.3, encoding Transcription factor SPT20 homolog (Q8NEM7). Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. It is a selective cancer dependency (DepMap: 11.8% of cell lines).

Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of gluconeogenesis and positive regulation of transcription by RNA polymerase II. Part of SAGA-type complex.

Source: NCBI Gene 55578 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 123 total
• Phenotypes (HPO): 1
• Cancer dependency (DepMap): dependent in 11.8% of screened cell lines
• MANE Select transcript: NM_001014286

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20596
Approved symbol	SUPT20H
Name	SPT20 homolog, SAGA complex component
Location	13q13.3
Locus type	gene with protein product
Status	Approved
Aliases	SPT20, bA421P11.4, P38IP
Ensembl gene	ENSG00000102710
Ensembl biotype	protein_coding
OMIM	613417
Entrez	55578

Gene structure

Transcript identifiers

Ensembl transcripts: 53 — 37 protein_coding, 7 retained_intron, 7 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000350612, ENST00000356185, ENST00000360252, ENST00000464572, ENST00000464744, ENST00000466563, ENST00000469488, ENST00000470359, ENST00000471868, ENST00000472948, ENST00000473871, ENST00000475892, ENST00000476109, ENST00000476539, ENST00000478911, ENST00000483241, ENST00000484078, ENST00000488590, ENST00000490602, ENST00000490716, ENST00000493537, ENST00000495071, ENST00000497318, ENST00000858400, ENST00000858401, ENST00000858402, ENST00000858403, ENST00000858404, ENST00000858405, ENST00000858406, ENST00000858407, ENST00000858408, ENST00000858409, ENST00000858410, ENST00000858411, ENST00000858412, ENST00000858413, ENST00000932737, ENST00000932738, ENST00000932739, ENST00000932740, ENST00000932741, ENST00000932742, ENST00000932743, ENST00000932744, ENST00000969156, ENST00000969157, ENST00000969158, ENST00000969159, ENST00000969160, ENST00000969161, ENST00000969162, ENST00000969163

RefSeq mRNA: 5 — MANE Select: NM_001014286 NM_001014286, NM_001278480, NM_001278481, NM_001278482, NM_017569

CCDS: CCDS31959, CCDS61311, CCDS9362

Canonical transcript exons

ENST00000350612 — 26 exons

Exon	Start	End
ENSE00003466297	37031739	37031895
ENSE00003482985	37026790	37026816
ENSE00003502358	37031567	37031623
ENSE00003503267	37021448	37021602
ENSE00003519410	37024340	37024442
ENSE00003534794	37047878	37047936
ENSE00003544703	37012192	37012297
ENSE00003565426	37028148	37028305
ENSE00003584202	37017245	37017364
ENSE00003589981	37022011	37022080
ENSE00003591174	37025320	37025437
ENSE00003598275	37040576	37040692
ENSE00003604488	37033449	37033588
ENSE00003606180	37051488	37051583
ENSE00003608674	37029765	37029836
ENSE00003615009	37024035	37024193
ENSE00003640589	37045247	37045373
ENSE00003641084	37048564	37048599
ENSE00003647780	37026204	37026236
ENSE00003650364	37010552	37010655
ENSE00003657494	37047535	37047601
ENSE00003671136	37019342	37019397
ENSE00003677850	37044078	37044181
ENSE00003787359	37040405	37040458
ENSE00003841810	37059559	37059688
ENSE00003847092	37009312	37009809

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 96.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.8896 / max 142.8032, expressed in 1817 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
136816	26.4546	1816
136815	0.1746	55
136814	0.1124	34
136817	0.1057	12
136813	0.0422	8

Top tissues by expression

293 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	96.07	gold quality
right testis	UBERON:0004534	95.66	gold quality
right uterine tube	UBERON:0001302	95.62	gold quality
ganglionic eminence	UBERON:0004023	95.52	gold quality
testis	UBERON:0000473	95.47	gold quality
ventricular zone	UBERON:0003053	95.41	gold quality
adrenal tissue	UBERON:0018303	95.26	gold quality
endocervix	UBERON:0000458	94.77	gold quality
cortical plate	UBERON:0005343	94.57	gold quality
right ovary	UBERON:0002118	94.49	gold quality
left ovary	UBERON:0002119	94.40	gold quality
adenohypophysis	UBERON:0002196	94.27	gold quality
body of uterus	UBERON:0009853	94.26	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	93.98	gold quality
cerebellar hemisphere	UBERON:0002245	93.78	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.72	gold quality
calcaneal tendon	UBERON:0003701	93.65	gold quality
cerebellar cortex	UBERON:0002129	93.55	gold quality
metanephros cortex	UBERON:0010533	93.55	gold quality
ectocervix	UBERON:0012249	93.53	gold quality
pituitary gland	UBERON:0000007	93.41	gold quality
muscle layer of sigmoid colon	UBERON:0035805	93.32	gold quality
left lobe of thyroid gland	UBERON:0001120	93.22	gold quality
right lobe of thyroid gland	UBERON:0001119	93.20	gold quality
colonic epithelium	UBERON:0000397	93.17	gold quality
body of pancreas	UBERON:0001150	93.16	gold quality
rectum	UBERON:0001052	93.11	gold quality
ovary	UBERON:0000992	92.97	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.95	gold quality
stromal cell of endometrium	CL:0002255	92.95	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.02
E-CURD-112	yes	5.70

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

6 targets.

Target	Regulation
AKR1C1
CGRRF1
CYP21A1P
CYP2C9
LTF
MAPK14

miRNA regulators (miRDB)

30 targeting SUPT20H, 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-3924	100.00	72.09	2394
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-370-5P	99.78	66.81	706
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-888-3P	99.53	69.77	1057
HSA-MIR-4696	99.48	67.48	1040
HSA-MIR-142-5P	99.48	70.92	2416
HSA-MIR-5590-3P	99.48	70.91	2429
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-888-5P	99.30	70.15	1855
HSA-MIR-642A-3P	99.23	67.67	1258
HSA-MIR-642B-3P	99.23	67.67	1258
HSA-MIR-3908	98.75	67.31	1160
HSA-MIR-581	98.39	67.42	835
HSA-MIR-12120	98.05	68.44	1768
HSA-MIR-6730-3P	97.03	67.54	889

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 11.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 9)

• mRNA is down-regulated in human prostate cancer, also described as C13 (PMID:11340631)
• Novel transcription factors identified in human CD34 antigen-positive hematopoietic stem cells. (PMID:12070015)
• C13orf19 mRNA is down-regulated in matched prostate tissues compared to prostate carcinoma tissues (PMID:15978328)
• C13orf19 is expressed independently of the androgen. No interaction between C13orf19 and p38MAPK was identified. (PMID:16685401)
• hSPT20 and other hSAGA subunits, together with RNA polymerase II, are specifically recruited to genes induced by endoplasmic reticulum (ER) stress. (PMID:19114550)
• Manipulation of p38IP and p38alpha alters mAtg9 localization, suggesting p38alpha regulates, through p38IP, the starvation-induced mAtg9 trafficking to forming autophagosomes. (PMID:19893488)
• p38IP inhibits ubiquitination-induced GCN5 degradation and therefore promotes alpha-tubulin acetylation, facilitating spindle formation and G2/M progression. (PMID:24220028)
• provide the first report that p38-p38IP is required for the Snail-induced E-cadherin down-regulation and cell invasion in HNSCC (PMID:27531877)
• Our results indicate that FAM48A is a kind of sensor that is required for compensatory autophagy induction upon proteasome impairment. (PMID:31210371)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	supt20	ENSDARG00000078658
mus_musculus	Supt20	ENSMUSG00000027751
rattus_norvegicus	Supt20h	ENSRNOG00000059480
drosophila_melanogaster	Spt20	FBGN0036374

Paralogs (2): SUPT20HL2 (ENSG00000223611), SUPT20HL1 (ENSG00000223731)

Protein

Protein identifiers

Transcription factor SPT20 homolog — Q8NEM7 (reviewed: Q8NEM7)

Alternative names: p38-interacting protein

All UniProt accessions (5): Q8NEM7, B4E2D5, C9JQS2, H7C5F9, R4GND2

UniProt curated annotations — full annotation on UniProt →

Function. Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down-regulation of E-cadherin during gastrulation by regulating E-cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by FGF signaling and Snail. Required for starvation-induced ATG9A trafficking during autophagy.

Subunit / interactions. Interacts with MAPK14. Interacts with ATG9A.

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in testis, moderately in brain and pituitary gland. Expressed in several fetal tissues, including lung, brain, thymus and kidney. Expression is down-regulated in malignant prostate tissues.

Similarity. Belongs to the SPT20 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8NEM7-1	1	yes
Q8NEM7-2	2
Q8NEM7-3	3

RefSeq proteins (5): NP_001014308, NP_001265409, NP_001265410, NP_001265411, NP_060039 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021950	Spt20	Family
IPR046468	Spt20-like_SEP	Domain

Pfam: PF12090

UniProt features (49 total): helix 14, strand 13, region of interest 4, modified residue 4, splice variant 4, compositionally biased region 4, sequence variant 2, turn 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
9RDK	ELECTRON MICROSCOPY	2.41
7KTR	ELECTRON MICROSCOPY	2.93
8H7G	ELECTRON MICROSCOPY	3.7
7KTS	ELECTRON MICROSCOPY	19.09

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NEM7-F1	60.16	0.13

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 (4): 494, 519, 524, 296

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-3214847	HATs acetylate histones
R-HSA-3247509	Chromatin modifying enzymes
R-HSA-4839726	Chromatin organization

MSigDB gene sets: 147 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_REGULATION_OF_DNA_REPAIR, chr13q13, MODULE_205, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_RNA_SPLICING, GOBP_GASTRULATION, GOBP_DNA_DAMAGE_RESPONSE, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_STRESS, GOBP_EMBRYO_DEVELOPMENT, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN

GO Biological Process (6): regulation of DNA repair (GO:0006282), regulation of transcription by RNA polymerase II (GO:0006357), autophagy (GO:0006914), gastrulation (GO:0007369), regulation of RNA splicing (GO:0043484), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (2): transcription coregulator activity (GO:0003712), protein binding (GO:0005515)

GO Cellular Component (3): SAGA complex (GO:0000124), nucleus (GO:0005634), SAGA-type complex (GO:0070461)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Chromatin modifying enzymes	1
Chromatin organization	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
DNA repair	1
regulation of DNA metabolic process	1
regulation of cellular response to stress	1
transcription by RNA polymerase II	1
catabolic process	1
transmembrane transport	1
process utilizing autophagic mechanism	1
ectoderm formation	1
endoderm formation	1
mesoderm formation	1
embryonic morphogenesis	1
RNA splicing	1
regulation of gene expression	1
regulation of primary metabolic process	1
DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
transcription regulator activity	1
binding	1
SAGA-type complex	1
DUBm complex	1
peptidase complex	1
intracellular membrane-bounded organelle	1
histone acetyltransferase complex	1

Protein interactions and networks

STRING

1092 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SUPT20H	ATG9A	Q7Z3C6	949
SUPT20H	SUPT7L	O94864	933
SUPT20H	TAF6L	Q9Y6J9	857
SUPT20H	KAT2B	Q92831	842
SUPT20H	TAF6	P49848	841
SUPT20H	TADA3	O75528	837
SUPT20H	KAT2A	Q92830	830
SUPT20H	TAF9	Q16594	821
SUPT20H	TAF5	Q15542	816
SUPT20H	TAF10	Q12962	773
SUPT20H	TAF12	Q16514	766
SUPT20H	ATXN7	O15265	743
SUPT20H	TRRAP	Q9Y4A5	742
SUPT20H	TAF5L	O75529	739
SUPT20H	TADA2B	Q86TJ2	738

IntAct

74 interactions, top by confidence:

A	B	Type	Score
SGF29	NDC80	psi-mi:“MI:0914”(association)	0.840
MED23	MED19	psi-mi:“MI:2364”(proximity)	0.770
MAPK14	SUPT20H	psi-mi:“MI:0915”(physical association)	0.760
TAF12	TAF4	psi-mi:“MI:0914”(association)	0.760
SUPT20H	MAPK14	psi-mi:“MI:0915”(physical association)	0.760
TRRAP	ATXN7	psi-mi:“MI:0914”(association)	0.740
ATXN1	SUPT20H	psi-mi:“MI:0915”(physical association)	0.670
ATXN7L3	USP27X	psi-mi:“MI:0914”(association)	0.640
KPNA1	TCERG1	psi-mi:“MI:0914”(association)	0.640
TADA1	TADA3	psi-mi:“MI:0914”(association)	0.640
SUPT20H	ATXN7	psi-mi:“MI:0914”(association)	0.530
MYLK4	HSP90AA1	psi-mi:“MI:0914”(association)	0.530
TAF6L	SUPT3H	psi-mi:“MI:0914”(association)	0.530
TADA2B	SUPT3H	psi-mi:“MI:0914”(association)	0.530
SGF29	MATN2	psi-mi:“MI:0914”(association)	0.530
SUPT20H	TAF5L	psi-mi:“MI:0914”(association)	0.530
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
SUPT20H	RPLP2	psi-mi:“MI:0915”(physical association)	0.400
SUPT20H	PDIA3	psi-mi:“MI:0915”(physical association)	0.400
SUPT20H	MAPK1	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (199): SUPT20H (Protein-peptide), SUPT20H (Affinity Capture-MS), SUPT20H (Two-hybrid), ATG9A (Affinity Capture-Western), SUPT20H (Co-fractionation), SUPT20H (Affinity Capture-Western), SUPT20H (Affinity Capture-Western), MAPK14 (Affinity Capture-Western), SUPT20H (Affinity Capture-MS), SUPT20H (Affinity Capture-MS), SUPT20H (Affinity Capture-MS), SUPT20H (Affinity Capture-MS), SUPT20H (Affinity Capture-MS), SUPT20H (Affinity Capture-MS), SUPT20H (Affinity Capture-MS)

ESM2 similar proteins: A2RSY1, F1R7R1, O54972, O75069, O75151, O88873, P0CH95, P49140, P58929, Q02225, Q06455, Q13233, Q1LY51, Q24767, Q2VPU4, Q2YDD2, Q3KR73, Q499B3, Q4VGL6, Q5F3B1, Q5PQS6, Q5TC82, Q60416, Q60698, Q61909, Q62415, Q62739, Q66IV1, Q6F6B3, Q6NUC6, Q6NYU6, Q7Z3K3, Q80TJ7, Q80W04, Q8BZH4, Q8CHY6, Q8CID0, Q8K2L8, Q8NEM7, Q8TEK3

Diamond homologs: P0C7V6, Q3ZLR7, Q5R724, Q5ZM71, Q66HC7, Q7TT00, Q8NEM7, F4IDB2

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
SUPT20H	“form complex”	“SAGA complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 75 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
HATs acetylate histones	14	22.2×	5e-13
Chromatin organization	11	17.9×	3e-09
Chromatin modifying enzymes	12	17.4×	7e-10

GO biological processes:

GO term	Partners	Fold	FDR
regulation of DNA repair	16	60.5×	3e-22
regulation of RNA splicing	15	45.0×	7e-19
RNA polymerase II preinitiation complex assembly	6	22.3×	3e-05
positive regulation of transcription initiation by RNA polymerase II	5	18.6×	6e-04
transcription by RNA polymerase II	8	7.7×	6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

123 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	87
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3856 predictions. Top by Δscore:

Variant	Effect	Δscore
13:37009805:AACTG:A	acceptor_gain	1.0000
13:37009807:CTG:C	acceptor_gain	1.0000
13:37009808:TG:T	acceptor_gain	1.0000
13:37009810:C:CC	acceptor_gain	1.0000
13:37010497:A:AC	donor_gain	1.0000
13:37010498:C:CC	donor_gain	1.0000
13:37010550:A:AC	donor_gain	1.0000
13:37010551:C:CC	donor_gain	1.0000
13:37011558:CT:C	donor_gain	1.0000
13:37012186:ACCT:A	donor_loss	1.0000
13:37012188:CTA:C	donor_loss	1.0000
13:37012189:TA:T	donor_loss	1.0000
13:37012190:A:AC	donor_gain	1.0000
13:37012190:A:AT	donor_loss	1.0000
13:37012191:C:CC	donor_gain	1.0000
13:37012191:C:CT	donor_loss	1.0000
13:37012191:CCAG:C	donor_gain	1.0000
13:37012217:T:TA	donor_gain	1.0000
13:37012296:CC:C	acceptor_gain	1.0000
13:37012296:CCCTG:C	acceptor_loss	1.0000
13:37012297:CC:C	acceptor_gain	1.0000
13:37021598:CCCCA:C	acceptor_gain	1.0000
13:37021599:CCCA:C	acceptor_gain	1.0000
13:37021599:CCCAC:C	acceptor_gain	1.0000
13:37021600:CCAC:C	acceptor_gain	1.0000
13:37021601:CA:C	acceptor_gain	1.0000
13:37021603:C:CC	acceptor_gain	1.0000
13:37022100:C:CT	acceptor_gain	1.0000
13:37024031:TCACT:T	donor_loss	1.0000
13:37024032:CA:C	donor_loss	1.0000

AlphaMissense

5067 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:37040413:A:G	W187R	1.000
13:37040413:A:T	W187R	1.000
13:37040643:C:A	R149M	1.000
13:37040652:C:G	R146P	1.000
13:37040667:A:T	V141D	1.000
13:37040681:A:C	F136L	1.000
13:37040681:A:T	F136L	1.000
13:37040683:A:G	F136L	1.000
13:37044091:A:G	L128P	1.000
13:37044094:A:G	L127P	1.000
13:37044115:A:G	L120S	1.000
13:37045267:A:G	L91P	1.000
13:37045273:A:G	L89P	1.000
13:37045277:A:G	S88P	1.000
13:37045300:A:G	L80P	1.000
13:37045306:A:T	V78D	1.000
13:37033560:A:G	L199P	0.999
13:37033572:A:G	L195P	0.999
13:37040411:C:A	W187C	0.999
13:37040411:C:G	W187C	0.999
13:37040445:T:A	D176V	0.999
13:37040445:T:C	D176G	0.999
13:37040445:T:G	D176A	0.999
13:37040446:C:G	D176H	0.999
13:37040592:A:G	L166S	0.999
13:37040642:C:A	R149S	0.999
13:37040642:C:G	R149S	0.999
13:37040643:C:G	R149T	0.999
13:37040650:C:G	D147H	0.999
13:37040653:G:T	R146S	0.999

dbSNP variants (sampled 300 via entrez): RS1000006296 (13:37021753 T>A,C), RS1000040621 (13:37050112 T>C), RS1000061273 (13:37030122 T>A,C), RS1000111267 (13:37030412 T>C), RS1000129230 (13:37019081 C>A), RS1000221399 (13:37018876 T>C), RS1000417556 (13:37015947 C>T), RS1000442123 (13:37056042 A>G), RS1000452897 (13:37025846 CT>C), RS1000464400 (13:37020426 G>A,T), RS1000488726 (13:37057217 C>T), RS1000549009 (13:37057627 A>T), RS1000558691 (13:37020243 T>C), RS1000608296 (13:37060917 G>C), RS1000748994 (13:37049272 G>A)

Disease associations

OMIM: gene MIM:613417 | disease phenotypes: MIM:180300

GenCC curated gene-disease

Mondo (1): rheumatoid arthritis (MONDO:0008383)

Orphanet (1): NON RARE IN EUROPE: Rheumatoid arthritis (Orphanet:284130)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0001370	Rheumatoid arthritis

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001585_14	Breast size	6.000000e-06
GCST006102_10	Interleukin-10 levels	1.000000e-07
GCST90002401_56	Platelet distribution width	1.000000e-19

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004750	interleukin 10 measurement
EFO:0007984	platelet component distribution width

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D001172	Arthritis, Rheumatoid	C05.550.114.154; C05.799.114; C17.300.775.099; C20.111.199

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
FR900359	decreases phosphorylation	1
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
bisphenol A	decreases methylation	1
trichostatin A	increases expression	1
beta-lapachone	decreases expression	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
beta-methylcholine	affects expression	1
(E)-4-((2-N-(4-methoxybenzenesulfonyl)amino)stilbazole)1-oxide	decreases expression	1
abrine	increases expression	1
Sunitinib	decreases expression	1
Acrolein	affects cotreatment, increases expression, increases abundance	1
Air Pollutants	increases abundance, increases expression, affects cotreatment	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression, increases abundance	1
Caffeine	decreases phosphorylation	1
Doxorubicin	decreases expression	1
Emodin	increases expression	1
Ozone	increases abundance, affects cotreatment, increases expression	1
Vincristine	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	increases abundance, decreases expression	1
Volatile Organic Compounds	affects cotreatment, increases expression	1

Cellosaurus cell lines

4 cell lines: 3 embryonic stem cell, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A1Q5	SEES3-1V human FAM48A, clone1	Embryonic stem cell	Male
CVCL_A1Q6	SEES3-1V human FAM48A, clone2	Embryonic stem cell	Male
CVCL_A1Q7	SEES3-1V human FAM48A, clone3	Embryonic stem cell	Male
CVCL_B3IQ	Abcam HEK293T SUPT20H KO	Transformed cell line	Female

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT00056667	PHASE4	COMPLETED	Relaxation Response Training for the Treatment of Rheumatoid Arthritis
NCT00094341	PHASE4	COMPLETED	Preference of Rheumatoid Arthritis (RA) Patients of Enbrel® (Etanercept) Auto-Injector Versus Enbrel® Pre-Filled Syringes
NCT00099554	PHASE4	COMPLETED	Effectiveness and Safety of Enbrel® (Etanercept) in Rheumatoid Arthritis Subjects Who Have Failed Remicade® (Infliximab)
NCT00111410	PHASE4	COMPLETED	Evaluating the Effect of Anakinra (r-metHuIL-1ra) on Vaccine AntibodyResponse in Subjects With Rheumatoid Arthritis (RA)
NCT00115219	PHASE4	COMPLETED	Evaluating Efficacy and Safety of Etanercept 50 mg Twice Weekly (BIW) in Rheumatoid Arthritis (RA) Subjects Who Are Sub-Optimal Responders to Etanercept 50 mg Once Weekly (QW)
NCT00121043	PHASE4	COMPLETED	Evaluating Kineret® (Anakinra) in Rheumatoid Arthritis (RA) Subjects Using aSelf-Reported Questionnaire
NCT00132418	PHASE4	COMPLETED	Study of Enbrel in Rheumatoid Arthritis (RA) Subjects With Comorbid Disorders
NCT00157872	PHASE4	COMPLETED	A Study of Rofecoxib Versus Naproxen in the Treatment of Chinese Patient With Rheumatoid Arthritis (0966-231)
NCT00195494	PHASE4	COMPLETED	Study Comparing Etanercept and Methotrexate vs. Methotrexate Alone in Rheumatoid Arthritis
NCT00208364	PHASE4	TERMINATED	A Two Centre Study to Assess the Long-term Performance of the Pinnacle™ Cup With a Metal-on-Metal Bearing in Primary Total Hip Replacement
NCT00208377	PHASE4	TERMINATED	A Multi-centre Study to Assess the Long-term Performance of the DePuy ASR™ System in Primary Hip Resurfacing Surgery
NCT00208390	PHASE4	TERMINATED	A Multi-centre Study to Assess the Long-term Performance of the Summit™ Hip in Primary Total Hip Replacement
NCT00208429	PHASE4	WITHDRAWN	A Multi-centre Study to Assess the Long-term Performance of the Pinnacle™ Cup With a Polyethylene-on-metal Bearing in Primary Total Hip Replacement
NCT00208455	PHASE4	TERMINATED	A Multi-centre Study to Assess the Long-term Performance of the DePuy PROXIMA™ Hip in Primary Total Hip Replacement
NCT00209859	PHASE4	COMPLETED	Methotrexate and Cyclosporine in Treatment of Early Rheumatoid Arthritis
NCT00216177	PHASE4	UNKNOWN	Comparison of Adalimumab and Infliximab Treatment of Rheumatoid Arthritis
NCT00233558	PHASE4	TERMINATED	Open-Label Steroid Reduction Study of Adalimumab With Methotrexate in Patients With Active Rheumatoid Arthritis
NCT00234234	PHASE4	COMPLETED	Predictors of the Response to Adalimumab in Rheumatoid Arthritis
NCT00234897	PHASE4	COMPLETED	Efficacy of HUMIRA in Subjects With Active Rheumatoid Arthritis
NCT00244556	PHASE4	COMPLETED	Study Comparing Enbrel (Etanercept) Plus Methotrexate Versus Enbrel Alone in Active Rheumatoid Arthritis Despite Current Methotrexate Therapy
NCT00252668	PHASE4	COMPLETED	Study Evaluating the Combination of Etanercept and Methotrexate in Rheumatoid Arthritis Subjects
NCT00259610	PHASE4	COMPLETED	Treatment of Early Aggressive Rheumatoid Arthritis (TEAR)
NCT00291915	PHASE4	UNKNOWN	Multicenter Randomized Prospective Trial Comparing Methotrexate Alone or in Combination With Adalimumab in Early Arthritis
NCT00319917	PHASE4	COMPLETED	A Double Blind Placebo Controlled Study to Assess the Efficacy on Joint Damage in RA Patients
NCT00334620	PHASE4	COMPLETED	Effectiveness of Radon Spa Therapy in Multimodal Rehabilitative Treatment of Rheumatoid Arthritis
NCT00346294	PHASE4	COMPLETED	An Open-Label Study to Assess the Rate of Failure of an Enbrel® (Etanercept) SureClick™ Auto-injector in Subjects With Rheumatoid Arthritis
NCT00356473	PHASE4	COMPLETED	Effects of Atorvastatin on Disease Activity and HDL Cholesterol Function in Patients With Rheumatoid Arthritis
NCT00369187	PHASE4	COMPLETED	Study of a Large Protein Molecule Administered With Escalating Doses of Recombinant Human Hyaluronidase
NCT00385528	PHASE4	COMPLETED	Effects of a Multi-Faceted Psychiatric Intervention Targeted at the Complex Medically Ill: a Randomized Controlled Trial
NCT00396747	PHASE4	COMPLETED	A Comparison of Methotrexate Alone or Combined to Infliximab or to Pulse Methylprednisolone in Early Rheumatoid Arthritis: A Magnetic Resonance Imaging Study
NCT00420927	PHASE4	COMPLETED	Study of the Optimal Protocol for Methotrexate and Adalimumab Combination Therapy in Early Rheumatoid Arthritis
NCT00422227	PHASE4	COMPLETED	Study Comparing Etanercept With Usual DMARD Therapy in Subjects With Rheumatoid Arthritis in the Asia Pacific Region
NCT00424502	PHASE4	COMPLETED	A Study of MabThera (Rituximab) in Patients With Rheumatoid Arthritis Who Have Had an Inadequate Response to a TNF-Blocker.
NCT00434200	PHASE4	UNKNOWN	Rheumatoid Arthritis Patients in Training
NCT00439062	PHASE4	COMPLETED	Treatment of Rheumatoid Arthritis With Roxithromycin
NCT00447759	PHASE4	COMPLETED	The Standard Care Versus Celecoxib Outcome Trial
NCT00462072	PHASE4	COMPLETED	Centocor Microarray Study of Patients
NCT00462345	PHASE4	COMPLETED	A Study of MabThera (Rituximab) in Combination With Methotrexate in Patients With Rheumatoid Arthritis Who Have Had an Inadequate Response to Anti-TNF Therapies.
NCT00480272	PHASE4	COMPLETED	Prospective Study on Intensive Early Rheumatoid Arthritis Treatment
NCT00502853	PHASE4	COMPLETED	A Pilot Study of MabThera (Rituximab) Evaluated by MRI in Patients With Rheumatoid Arthritis.