RFXAP

Summary

RFXAP (regulatory factor X associated protein, HGNC:9988) is a protein-coding gene on chromosome 13q13.3, encoding Regulatory factor X-associated protein (O00287). Part of the RFX complex that binds to the X-box of MHC II promoters.

Major histocompatibility (MHC) class II molecules are transmembrane proteins that have a central role in development and control of the immune system. The protein encoded by this gene, along with regulatory factor X-associated ankyrin-containing protein and regulatory factor-5, forms a complex that binds to the X box motif of certain MHC class II gene promoters and activates their transcription. Once bound to the promoter, this complex associates with the non-DNA-binding factor MHC class II transactivator, which controls the cell type specificity and inducibility of MHC class II gene expression. Mutations in this gene have been linked to bare lymphocyte syndrome type II, complementation group D. Transcript variants utilizing different polyA signals have been found for this gene.

Source: NCBI Gene 5994 — RefSeq curated summary.

At a glance

• Gene–disease (curated): MHC class II deficiency (Definitive, ClinGen) — +1 more curated relationship
• GWAS associations: 2
• Clinical variants (ClinVar): 148 total — 14 pathogenic, 5 likely-pathogenic
• Phenotypes (HPO): 56
• Transcription factor: yes — 19 downstream targets (CollecTRI)
• MANE Select transcript: NM_000538

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9988
Approved symbol	RFXAP
Name	regulatory factor X associated protein
Location	13q13.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000133111
Ensembl biotype	protein_coding
OMIM	601861
Entrez	5994

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000255476, ENST00000472888

RefSeq mRNA: 1 — MANE Select: NM_000538 NM_000538

CCDS: CCDS9359

Canonical transcript exons

ENST00000255476 — 3 exons

Exon	Start	End
ENSE00000907430	36819222	36819957
ENSE00000907431	36825428	36825535
ENSE00001182855	36827643	36829104

Expression profiles

Bgee: expression breadth ubiquitous, 231 present calls, max score 89.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.1731 / max 108.5483, expressed in 1654 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
134777	7.8551	1642
134776	0.3180	169

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.76	gold quality
tendon of biceps brachii	UBERON:0008188	83.72	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.07	gold quality
ventricular zone	UBERON:0003053	81.32	gold quality
palpebral conjunctiva	UBERON:0001812	80.47	gold quality
cortical plate	UBERON:0005343	80.35	gold quality
mucosa of paranasal sinus	UBERON:0005030	78.09	gold quality
mucosa of stomach	UBERON:0001199	77.99	gold quality
cerebellar hemisphere	UBERON:0002245	77.85	gold quality
cerebellar cortex	UBERON:0002129	77.76	gold quality
right hemisphere of cerebellum	UBERON:0014890	77.74	gold quality
ganglionic eminence	UBERON:0004023	77.52	gold quality
germinal epithelium of ovary	UBERON:0001304	77.20	gold quality
body of uterus	UBERON:0009853	76.94	gold quality
islet of Langerhans	UBERON:0000006	76.63	gold quality
ovary	UBERON:0000992	76.48	gold quality
cerebellum	UBERON:0002037	76.36	gold quality
monocyte	CL:0000576	76.25	gold quality
muscle layer of sigmoid colon	UBERON:0035805	76.24	gold quality
left ovary	UBERON:0002119	76.04	gold quality
mononuclear cell	CL:0000842	76.01	gold quality
tibial artery	UBERON:0007610	75.96	gold quality
popliteal artery	UBERON:0002250	75.94	gold quality
right ovary	UBERON:0002118	75.90	gold quality
leukocyte	CL:0000738	75.84	gold quality
endocervix	UBERON:0000458	75.83	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	75.68	gold quality
tibia	UBERON:0000979	75.64	gold quality
gastrocnemius	UBERON:0001388	75.49	gold quality
tendon	UBERON:0000043	75.45	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.94

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

19 targets.

Target	Regulation
CD74
CIITA
HLA-DMA	Unknown
HLA-DMB	Unknown
HLA-DOA	Unknown
HLA-DOB	Unknown
HLA-DPA1	Unknown
HLA-DPB1	Unknown
HLA-DQA1	Unknown
HLA-DQA2	Unknown
HLA-DQB1	Unknown
HLA-DQB2	Unknown
HLA-DRA	Unknown
HLA-DRB1	Unknown
HLA-DRB3	Unknown
HLA-DRB4	Unknown
HLA-DRB5	Unknown
HLA-E	Unknown
SMARCA4

miRNA regulators (miRDB)

89 targeting RFXAP, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3692-3P	99.98	70.27	2139
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-590-3P	99.96	74.34	6478
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-5682	99.89	72.56	1005
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-2052	99.79	69.37	2031

Literature-anchored findings (GeneRIF, showing 9)

• The identification of nuclear import and export sites on RFX molecules provides potential targets to modulate MHC class II expression. (PMID:15210800)
• Only the C-terminal half of the protein is conserved among vertebrates. The C-terminal third of RFXAP, with an extensive glutamine-rich tract, could rescue HLA-DR, but not HLA-DQ or HLA-DP expression in a bare lymphocyte syndrome cell line. (PMID:16337482)
• The transcriptional silent state of RFXAP correlated with reduced recruitment of RNA polymerase II to RFXAP chromatin in the MHC-II deficiency patient. (PMID:18336911)
• RFXAP and RFXB have roles in relieving autoinhibition of RFX5 (PMID:18723135)
• the interaction between RFX5 and RFXAP promote folding of a poorly structured region ofRFXAP, which is required for high affinity binding of RFXB to the RFX5.RFXAP complex (PMID:19274739)
• Study demonstrates that coordinate loss of MHCII expression in OCI-Ly2 DLBCL cells is associated with an 11-base deletion in the cDNA encoding RFX-AP, that is required for activating MHCII transcription. (PMID:20024540)
• RFXAP(C) consists of two alpha-helices that form a V-shaped structure that packs within the RFX5(N)(2) staple. (PMID:20732328)
• Data show a negative correlation between microRNA miR-212-3p and regulatory factor X-associated protein (RFXAP) in pancreatic cancer (PC) tissue. (PMID:26337469)
• Fisetin inhibits proliferation of pancreatic adenocarcinoma by inducing DNA damage via RFXAP/KDM4A-dependent histone H3K36 demethylation. (PMID:33093461)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	rfxap	ENSDARG00000076891
mus_musculus	Rfxap	ENSMUSG00000036615
rattus_norvegicus	Rfxap	ENSRNOG00000064105

Protein

Protein identifiers

Regulatory factor X-associated protein — O00287 (reviewed: O00287)

Alternative names: RFX DNA-binding complex 36 kDa subunit

All UniProt accessions (1): O00287

UniProt curated annotations — full annotation on UniProt →

Function. Part of the RFX complex that binds to the X-box of MHC II promoters.

Subunit / interactions. The RFX heterotetrameric complex consists of 2 molecules of RFX5 and one each of RFXAP and RFX-B/RFXANK; with each subunit representing a separate complementation group. RFX forms cooperative DNA binding complexes with X2BP and CBF/NF-Y. RFX associates with CIITA to form an active transcriptional complex.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitous.

Post-translational modifications. Phosphorylated.

Disease relevance. MHC class II deficiency 4 (MHC2D4) [MIM:620817] An autosomal recessive disorder characterized by immunodeficiency, failure to thrive, and recurrent bacterial, viral, fungal and parasitic infections from birth, usually affecting the respiratory and gastrointestinal tract. Patients may die in infancy or early childhood. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The C-terminal domain is necessary for the RFX complex formation.

RefSeq proteins (1): NP_000529* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029316	RFXAP_RFXANK-bd	Domain
IPR038308	RFXAP_C_sf	Homologous_superfamily

Pfam: PF15289

UniProt features (12 total): region of interest 4, helix 2, chain 1, short sequence motif 1, compositionally biased region 1, cross-link 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2KW3	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O00287-F1	66.51	0.25

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): 198

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 211 (showing top): FISCHER_G1_S_CELL_CYCLE, BROWNE_HCMV_INFECTION_16HR_UP, chr13q13, MORF_EPHA7, KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION, MORF_DCC, GOCC_RNA_POLYMERASE_II_TRANSCRIPTION_REGULATOR_COMPLEX, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, GOCC_TRANSCRIPTION_REGULATOR_COMPLEX, GOCC_RIBONUCLEOPROTEIN_GRANULE, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C, KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_UP, TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_UP

GO Biological Process (4): regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of MHC class II biosynthetic process (GO:0045348), positive regulation of transcription by RNA polymerase II (GO:0045944), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (4): DNA binding (GO:0003677), RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), nuclear speck (GO:0016607), RNA polymerase II transcription regulator complex (GO:0090575)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	2
positive regulation of macromolecule biosynthetic process	1
MHC class II biosynthetic process	1
regulation of MHC class II biosynthetic process	1
regulation of transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	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
binding	1
intracellular membrane-bounded organelle	1
nuclear ribonucleoprotein granule	1
transcription regulator complex	1
nuclear protein-containing complex	1

Protein interactions and networks

STRING

472 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RFXAP	RFXANK	O14593	999
RFXAP	RFX5	P48382	999
RFXAP	CIITA	P33076	970
RFXAP	RFX1	P22670	961
RFXAP	CREB1	P16220	933
RFXAP	NLRC5	Q86WI3	728
RFXAP	ANK3	Q12955	726
RFXAP	ANK2	Q01484	725
RFXAP	NFYC	Q13952	725
RFXAP	ANK1	P16157	724
RFXAP	RFX2	P48378	677
RFXAP	NFYA	P23511	670
RFXAP	HLA-DRA	P01903	633
RFXAP	POU3F4	P49335	587
RFXAP	NFYB	P25208	584

IntAct

34 interactions, top by confidence:

A	B	Type	Score
RFX5	RFXAP	psi-mi:“MI:0914”(association)	0.880
RFX5	RFXAP	psi-mi:“MI:0407”(direct interaction)	0.880
RFXAP	RFX5	psi-mi:“MI:0407”(direct interaction)	0.880
RFX5	RFXAP	psi-mi:“MI:0915”(physical association)	0.880
RFXANK	RFXAP	psi-mi:“MI:0914”(association)	0.780
RFXANK	RFXAP	psi-mi:“MI:0407”(direct interaction)	0.780
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
RFXAP	H2AC12	psi-mi:“MI:0915”(physical association)	0.400
RFXAP	H2AC4	psi-mi:“MI:0915”(physical association)	0.400
RFXAP	H2BC9	psi-mi:“MI:0915”(physical association)	0.400
EPS8	RFXAP	psi-mi:“MI:0915”(physical association)	0.370
Rfx5	MRPL27	psi-mi:“MI:0914”(association)	0.350
ANKRA2	RFXAP	psi-mi:“MI:0914”(association)	0.350
RFXANK	BLTP3B	psi-mi:“MI:0914”(association)	0.350
SLC16A11	ESYT2	psi-mi:“MI:0914”(association)	0.350
SH2D3A	RFXAP	psi-mi:“MI:0914”(association)	0.350
HNF4A	TAF4	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (33): RFXAP (Synthetic Growth Defect), RFXAP (Affinity Capture-MS), RFXAP (Affinity Capture-MS), RFXAP (Affinity Capture-MS), RFXAP (Affinity Capture-MS), RFXAP (Affinity Capture-MS), RFX5 (Two-hybrid), RFXAP (Proximity Label-MS), RFXAP (Affinity Capture-MS), RFXAP (Proximity Label-MS), HIST1H2BH (Proximity Label-MS), HIST1H2AH (Proximity Label-MS), RFXAP (Reconstituted Complex), RFXAP (Affinity Capture-Western), RFXAP (Affinity Capture-MS)

ESM2 similar proteins: A0A287BDC1, A8YXY8, B1AXD8, B3F209, B3KU38, B5DF41, O00287, O14503, O15079, O35185, O54972, P03966, P04198, P12755, P18444, P26014, Q0D2I5, Q25C79, Q2KJ58, Q3MHV6, Q3UR85, Q50H33, Q53H80, Q5BL57, Q5EA15, Q5FWN7, Q5RAI7, Q60591, Q60698, Q61976, Q63379, Q68FF7, Q6GQB5, Q6ZWB6, Q7ZY70, Q8BXL9, Q8CEG5, Q8CI08, Q8N228, Q8ND83

Diamond homologs: O00287, Q8VCG9

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
RFXAP	“form complex”	“RFX complex”	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	14
Likely pathogenic	5
Uncertain significance	78
Likely benign	39
Benign	7

Top pathogenic / likely-pathogenic (19)

Variant ID	HGVS	Classification
1068494	NM_000538.4(RFXAP):c.203dup (p.Lys69fs)	Pathogenic
1068569	NM_000538.4(RFXAP):c.188del (p.Gly63fs)	Pathogenic
1459705	NM_000538.4(RFXAP):c.359del (p.Gly120fs)	Pathogenic
2570862	NM_000538.4(RFXAP):c.634C>T (p.Gln212Ter)	Pathogenic
3236735	NM_000538.4(RFXAP):c.350del (p.His117fs)	Pathogenic
3236736	NM_000538.4(RFXAP):c.467del (p.Gln156fs)	Pathogenic
3236737	NM_000538.4(RFXAP):c.219C>G (p.Tyr73Ter)	Pathogenic
4699880	NM_000538.4(RFXAP):c.359dup (p.Glu121fs)	Pathogenic
4725937	NM_000538.4(RFXAP):c.244G>T (p.Glu82Ter)	Pathogenic
4734127	NM_000538.4(RFXAP):c.279dup (p.Asp94fs)	Pathogenic
7649	NM_000538.4(RFXAP):c.302dup (p.Gly102fs)	Pathogenic
7650	NM_000538.4(RFXAP):c.392dup (p.Ser132fs)	Pathogenic
7651	NM_000538.4(RFXAP):c.368del (p.Ser123fs)	Pathogenic
7652	NM_000538.4(RFXAP):c.163C>T (p.Gln55Ter)	Pathogenic
208152	NM_000538.4(RFXAP):c.323T>A (p.Leu108Ter)	Likely pathogenic
3065776	NM_000538.4(RFXAP):c.287C>A (p.Ser96Ter)	Likely pathogenic
3575882	NM_000538.4(RFXAP):c.52_100del (p.Val18fs)	Likely pathogenic
3575885	NM_000538.4(RFXAP):c.696_700del (p.Asn232fs)	Likely pathogenic
4804483	NM_000538.4(RFXAP):c.601-2A>T	Likely pathogenic

SpliceAI

331 predictions. Top by Δscore:

Variant	Effect	Δscore
13:36819954:CGAG:C	donor_loss	1.0000
13:36819955:GAGGT:G	donor_loss	1.0000
13:36819956:AGG:A	donor_loss	1.0000
13:36819957:GGT:G	donor_loss	1.0000
13:36819958:GTATC:G	donor_loss	1.0000
13:36819959:T:G	donor_loss	1.0000
13:36827640:A:AG	acceptor_gain	1.0000
13:36827640:AAGTC:A	acceptor_gain	1.0000
13:36827641:A:AG	acceptor_gain	1.0000
13:36827642:G:GG	acceptor_gain	1.0000
13:36827642:GTC:G	acceptor_gain	1.0000
13:36819955:G:GT	donor_gain	0.9900
13:36825427:GGAAA:G	acceptor_gain	0.9900
13:36826974:GA:G	donor_gain	0.9900
13:36826976:G:GG	donor_gain	0.9900
13:36827639:TAAGT:T	acceptor_loss	0.9900
13:36827641:AGTC:A	acceptor_gain	0.9900
13:36827642:G:GT	acceptor_loss	0.9900
13:36827642:GT:G	acceptor_gain	0.9900
13:36827642:GTCG:G	acceptor_gain	0.9900
13:36827642:GTCGT:G	acceptor_gain	0.9900
13:36825531:GACTG:G	donor_gain	0.9800
13:36819955:GAG:G	donor_gain	0.9600
13:36827644:C:A	acceptor_gain	0.9500
13:36819958:G:GG	donor_gain	0.9400
13:36825415:T:G	acceptor_gain	0.9400
13:36825421:A:AG	acceptor_gain	0.9400
13:36825418:T:G	acceptor_gain	0.9300
13:36819971:C:G	donor_gain	0.9000
13:36825422:TCCCA:T	acceptor_loss	0.9000

AlphaMissense

1763 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:36819778:T:C	C141R	1.000
13:36819793:T:A	C146S	1.000
13:36819793:T:C	C146R	1.000
13:36819794:G:C	C146S	1.000
13:36819835:T:A	W160R	1.000
13:36819835:T:C	W160R	1.000
13:36819837:G:C	W160C	1.000
13:36819837:G:T	W160C	1.000
13:36819839:T:C	M161T	1.000
13:36819841:T:A	C162S	1.000
13:36819841:T:C	C162R	1.000
13:36819842:G:A	C162Y	1.000
13:36819842:G:C	C162S	1.000
13:36819842:G:T	C162F	1.000
13:36819843:C:G	C162W	1.000
13:36819844:A:G	K163E	1.000
13:36819846:G:C	K163N	1.000
13:36819846:G:T	K163N	1.000
13:36819850:C:A	H165N	1.000
13:36819850:C:G	H165D	1.000
13:36819851:A:G	H165R	1.000
13:36819852:C:A	H165Q	1.000
13:36819852:C:G	H165Q	1.000
13:36819853:C:A	R166S	1.000
13:36819854:G:C	R166P	1.000
13:36819856:A:G	N167D	1.000
13:36819858:C:A	N167K	1.000
13:36819858:C:G	N167K	1.000
13:36819865:T:C	Y170H	1.000
13:36819866:A:G	Y170C	1.000

dbSNP variants (sampled 300 via entrez): RS1000071487 (13:36822471 G>C), RS1000246768 (13:36821048 G>A,T), RS1000671267 (13:36826342 C>T), RS1000852141 (13:36819407 G>C,T), RS1001173984 (13:36821734 T>C), RS1001254976 (13:36829384 A>G), RS1001284335 (13:36819244 C>A,G,T), RS1001352582 (13:36828945 C>G,T), RS1001403435 (13:36829272 T>C), RS1001774460 (13:36817658 T>C), RS1001829995 (13:36818097 A>T), RS1002078351 (13:36824553 G>A), RS1002681190 (13:36822807 T>C), RS1003226919 (13:36823091 A>G), RS1003485256 (13:36828605 A>C,G)

Disease associations

OMIM: gene MIM:601861 | disease phenotypes: MIM:209920, MIM:620817

GenCC curated gene-disease

Disease	Classification	Inheritance
MHC class II deficiency	Strong	Autosomal recessive
MHC class II deficiency 4	Strong	Autosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
MHC class II deficiency	Definitive	AR

Mondo (3): MHC class II deficiency (MONDO:0008855), MHC class II deficiency 4 (MONDO:0971015), MHC class II deficiency 1 (MONDO:0971005)

Orphanet (1): Immunodeficiency by defective expression of MHC class II (Orphanet:572)

HPO phenotypes

56 total (30 of 56 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000246	Sinusitis
HP:0000371	Acute otitis media
HP:0000403	Recurrent otitis media
HP:0000988	Skin rash
HP:0001251	Ataxia
HP:0001252	Hypotonia
HP:0001260	Dysarthria
HP:0001263	Global developmental delay
HP:0001508	Failure to thrive
HP:0001744	Splenomegaly
HP:0001875	Decreased total neutrophil count
HP:0001876	Pancytopenia
HP:0001890	Autoimmune hemolytic anemia
HP:0001904	Autoimmune neutropenia
HP:0001973	Autoimmune thrombocytopenia
HP:0001999	Abnormal facial shape
HP:0002014	Diarrhea
HP:0002066	Gait ataxia
HP:0002205	Recurrent respiratory infections
HP:0002240	Hepatomegaly
HP:0002718	Recurrent bacterial infections
HP:0002720	Decreased circulating IgA concentration
HP:0002726	Recurrent Staphylococcus aureus infections
HP:0002728	Chronic mucocutaneous candidiasis
HP:0002841	Recurrent fungal infections
HP:0002850	Decreased circulating total IgM
HP:0002960	Autoimmunity
HP:0003139	Panhypogammaglobulinemia
HP:0003347	Impaired lymphocyte transformation with phytohemagglutinin

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST002892_13	Perioperative myocardial infarction in coronary artery bypass surgery	6.000000e-06
GCST009391_236	Metabolite levels	5.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010493	glycodeoxycholate measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C537079	Bare lymphocyte syndrome 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

45 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, decreases methylation	3
trichostatin A	affects cotreatment, decreases expression	2
sodium arsenite	affects cotreatment, decreases expression, increases abundance	2
Tetrachlorodibenzodioxin	decreases expression	2
Valproic Acid	decreases expression	2
Particulate Matter	increases abundance, increases expression	2
methylmercuric chloride	decreases expression	1
bisphenol A	affects cotreatment, increases methylation	1
sodium arsenate	decreases expression, increases abundance	1
arsenite	decreases expression, increases abundance	1
monomethylarsonic acid	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
arsenic acid	decreases expression, increases abundance	1
ferrous chloride	decreases expression	1
Am 580	decreases expression	1
CGP 52608	affects binding, increases reaction	1
monomethylarsonous acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
dimethylmonothioarsinic acid	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Rosiglitazone	decreases expression	1
Sunitinib	increases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Leflunomide	decreases expression	1
Acetaldehyde	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Atrazine	decreases expression	1

Cellosaurus cell lines

13 cell lines: 10 transformed cell line, 3 embryonic stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_A5V9	SEES3-1V human RFXAP, clone1	Embryonic stem cell	Male
CVCL_A5W0	SEES3-1V human RFXAP, clone2	Embryonic stem cell	Male
CVCL_A5W1	SEES3-1V human RFXAP, clone3	Embryonic stem cell	Male
CVCL_B7KA	VIP2	Transformed cell line	Male
CVCL_B7LG	ZM fibroblast	Transformed cell line
CVCL_B7LH	ZM LCL	Transformed cell line
CVCL_B7LJ	ABI	Transformed cell line
CVCL_B7LK	DA	Transformed cell line	Male
CVCL_B7LL	AkO	Transformed cell line
CVCL_B7LM	ShA	Transformed cell line

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01652092	Not specified	ACTIVE_NOT_RECRUITING	Allogeneic Hematopoietic Stem Cell Transplant for Patients With Primary Immune Deficiencies
NCT04251325	Not specified	UNKNOWN	Socio-demographic Characteristics of Basic Life Support Course Participants
NCT04353089	Not specified	UNKNOWN	Geographical Association Between Basic Life Support Courses, Bystander Cardiopulmonary Resuscitation and Survival