Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	5993
Gene name Gene Name - the full gene name approved by the HGNC.	Regulatory factor X5
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	RFX5
Synonyms (NCBI Gene) Gene synonyms aliases	MHC2D3, MHC2D5
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1q21.3
Summary Summary of gene provided in NCBI Entrez Gene.	A lack of MHC-II expression results in a severe immunodeficiency syndrome called MHC-II deficiency, or the bare lymphocyte syndrome (BLS; MIM 209920). At least 4 complementation groups have been identified in B-cell lines established from patients with BL

Show/Hide all(7)

SNP ID	Visualize variation	Clinical significance	Consequence
rs137853099	C>T	Pathogenic, uncertain-significance	5 prime UTR variant, missense variant, coding sequence variant
rs748270285	C>T	Pathogenic	Splice acceptor variant
rs1557831362	G>A	Pathogenic	Coding sequence variant, synonymous variant
rs1571256140	->G	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1571260017	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs1571260171	T>C	Likely-pathogenic	Splice acceptor variant
rs1571262081	->A	Pathogenic	Coding sequence variant, stop gained, 5 prime UTR variant

Show/Hide all(246)

miRTarBase ID	miRNA	Experiments	Reference
MIRT026061	hsa-miR-196a-5p	Sequencing	20371350
MIRT032137	hsa-let-7d-5p	Sequencing	20371350
MIRT042366	hsa-miR-484	CLASH	23622248
MIRT439779	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT439779	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT1302443	hsa-miR-1253	CLIP-seq
MIRT1302444	hsa-miR-130a	CLIP-seq
MIRT1302445	hsa-miR-130b	CLIP-seq
MIRT1302446	hsa-miR-186	CLIP-seq
MIRT1302447	hsa-miR-19a	CLIP-seq
MIRT1302448	hsa-miR-19b	CLIP-seq
MIRT1302449	hsa-miR-301a	CLIP-seq
MIRT1302450	hsa-miR-301b	CLIP-seq
MIRT1302451	hsa-miR-3154	CLIP-seq
MIRT1302452	hsa-miR-3666	CLIP-seq
MIRT1302453	hsa-miR-3677-5p	CLIP-seq
MIRT1302454	hsa-miR-4295	CLIP-seq
MIRT1302455	hsa-miR-4512	CLIP-seq
MIRT1302456	hsa-miR-454	CLIP-seq
MIRT1302457	hsa-miR-4662a-5p	CLIP-seq
MIRT1302458	hsa-miR-4757-5p	CLIP-seq
MIRT1302459	hsa-miR-518a-5p	CLIP-seq
MIRT1302460	hsa-miR-519a	CLIP-seq
MIRT1302461	hsa-miR-519b-3p	CLIP-seq
MIRT1302462	hsa-miR-519c-3p	CLIP-seq
MIRT1302463	hsa-miR-527	CLIP-seq
MIRT1302464	hsa-miR-663b	CLIP-seq
MIRT1302465	hsa-miR-885-3p	CLIP-seq
MIRT1302443	hsa-miR-1253	CLIP-seq
MIRT1302446	hsa-miR-186	CLIP-seq
MIRT1302466	hsa-miR-1910	CLIP-seq
MIRT1302467	hsa-miR-28-5p	CLIP-seq
MIRT1302468	hsa-miR-3139	CLIP-seq
MIRT1302469	hsa-miR-3150b-3p	CLIP-seq
MIRT1302470	hsa-miR-3653	CLIP-seq
MIRT1302471	hsa-miR-3658	CLIP-seq
MIRT1302472	hsa-miR-425	CLIP-seq
MIRT1302473	hsa-miR-4452	CLIP-seq
MIRT1302474	hsa-miR-4462	CLIP-seq
MIRT1302475	hsa-miR-4464	CLIP-seq
MIRT1302476	hsa-miR-4476	CLIP-seq
MIRT1302477	hsa-miR-4496	CLIP-seq
MIRT1302478	hsa-miR-4499	CLIP-seq
MIRT1302479	hsa-miR-4503	CLIP-seq
MIRT1302480	hsa-miR-451b	CLIP-seq
MIRT1302481	hsa-miR-4533	CLIP-seq
MIRT1302482	hsa-miR-4652-3p	CLIP-seq
MIRT1302457	hsa-miR-4662a-5p	CLIP-seq
MIRT1302483	hsa-miR-4676-5p	CLIP-seq
MIRT1302484	hsa-miR-4677-3p	CLIP-seq
MIRT1302485	hsa-miR-4679	CLIP-seq
MIRT1302486	hsa-miR-4689	CLIP-seq
MIRT1302487	hsa-miR-4695-3p	CLIP-seq
MIRT1302488	hsa-miR-4748	CLIP-seq
MIRT1302489	hsa-miR-4766-3p	CLIP-seq
MIRT1302490	hsa-miR-4784	CLIP-seq
MIRT1302491	hsa-miR-575	CLIP-seq
MIRT1302492	hsa-miR-601	CLIP-seq
MIRT1302493	hsa-miR-617	CLIP-seq
MIRT1302494	hsa-miR-708	CLIP-seq
MIRT1556988	hsa-miR-3140-3p	CLIP-seq
MIRT2089800	hsa-miR-1264	CLIP-seq
MIRT2089801	hsa-miR-128	CLIP-seq
MIRT1302466	hsa-miR-1910	CLIP-seq
MIRT2089802	hsa-miR-203	CLIP-seq
MIRT2089803	hsa-miR-3128	CLIP-seq
MIRT2089804	hsa-miR-3138	CLIP-seq
MIRT2089805	hsa-miR-3165	CLIP-seq
MIRT1302472	hsa-miR-425	CLIP-seq
MIRT2089806	hsa-miR-4259	CLIP-seq
MIRT2089807	hsa-miR-4456	CLIP-seq
MIRT1302474	hsa-miR-4462	CLIP-seq
MIRT1302476	hsa-miR-4476	CLIP-seq
MIRT2089808	hsa-miR-4639-3p	CLIP-seq
MIRT2089809	hsa-miR-4715-3p	CLIP-seq
MIRT2089810	hsa-miR-4715-5p	CLIP-seq
MIRT2089811	hsa-miR-509-3p	CLIP-seq
MIRT2089812	hsa-miR-562	CLIP-seq
MIRT2089805	hsa-miR-3165	CLIP-seq
MIRT1302443	hsa-miR-1253	CLIP-seq
MIRT2314678	hsa-miR-1262	CLIP-seq
MIRT2314679	hsa-miR-151-3p	CLIP-seq
MIRT2314680	hsa-miR-1827	CLIP-seq
MIRT1302467	hsa-miR-28-5p	CLIP-seq
MIRT1302468	hsa-miR-3139	CLIP-seq
MIRT1302469	hsa-miR-3150b-3p	CLIP-seq
MIRT2089805	hsa-miR-3165	CLIP-seq
MIRT2314681	hsa-miR-3675-3p	CLIP-seq
MIRT2314682	hsa-miR-3973	CLIP-seq
MIRT2314683	hsa-miR-411	CLIP-seq
MIRT1302472	hsa-miR-425	CLIP-seq
MIRT2314684	hsa-miR-4257	CLIP-seq
MIRT1302473	hsa-miR-4452	CLIP-seq
MIRT2089807	hsa-miR-4456	CLIP-seq
MIRT1302474	hsa-miR-4462	CLIP-seq
MIRT2314685	hsa-miR-4463	CLIP-seq
MIRT1302478	hsa-miR-4499	CLIP-seq
MIRT1302479	hsa-miR-4503	CLIP-seq
MIRT1302483	hsa-miR-4676-5p	CLIP-seq
MIRT2314686	hsa-miR-4701-3p	CLIP-seq
MIRT2089809	hsa-miR-4715-3p	CLIP-seq
MIRT1302490	hsa-miR-4784	CLIP-seq
MIRT2314687	hsa-miR-512-5p	CLIP-seq
MIRT2089812	hsa-miR-562	CLIP-seq
MIRT1302491	hsa-miR-575	CLIP-seq
MIRT1302494	hsa-miR-708	CLIP-seq
MIRT2089802	hsa-miR-203	CLIP-seq
MIRT2393652	hsa-miR-2110	CLIP-seq
MIRT2393653	hsa-miR-3150a-3p	CLIP-seq
MIRT2089805	hsa-miR-3165	CLIP-seq
MIRT2393654	hsa-miR-3175	CLIP-seq
MIRT2393655	hsa-miR-3929	CLIP-seq
MIRT1302472	hsa-miR-425	CLIP-seq
MIRT2393656	hsa-miR-4260	CLIP-seq
MIRT2393657	hsa-miR-4419b	CLIP-seq
MIRT2089807	hsa-miR-4456	CLIP-seq
MIRT1302474	hsa-miR-4462	CLIP-seq
MIRT2393658	hsa-miR-4478	CLIP-seq
MIRT2089809	hsa-miR-4715-3p	CLIP-seq
MIRT2393659	hsa-miR-485-5p	CLIP-seq
MIRT2393660	hsa-miR-939	CLIP-seq
MIRT2439892	hsa-miR-409-5p	CLIP-seq
MIRT2439893	hsa-miR-4704-5p	CLIP-seq
MIRT2610982	hsa-miR-1182	CLIP-seq
MIRT2610983	hsa-miR-1207-3p	CLIP-seq
MIRT1302443	hsa-miR-1253	CLIP-seq
MIRT2089800	hsa-miR-1264	CLIP-seq
MIRT2089801	hsa-miR-128	CLIP-seq
MIRT1302444	hsa-miR-130a	CLIP-seq
MIRT1302445	hsa-miR-130b	CLIP-seq
MIRT1302446	hsa-miR-186	CLIP-seq
MIRT1302447	hsa-miR-19a	CLIP-seq
MIRT1302448	hsa-miR-19b	CLIP-seq
MIRT2089802	hsa-miR-203	CLIP-seq
MIRT2610984	hsa-miR-2355-5p	CLIP-seq
MIRT2610985	hsa-miR-299-5p	CLIP-seq
MIRT1302449	hsa-miR-301a	CLIP-seq
MIRT1302450	hsa-miR-301b	CLIP-seq
MIRT2610986	hsa-miR-3120-5p	CLIP-seq
MIRT2610987	hsa-miR-3125	CLIP-seq
MIRT2089803	hsa-miR-3128	CLIP-seq
MIRT2089804	hsa-miR-3138	CLIP-seq
MIRT1556988	hsa-miR-3140-3p	CLIP-seq
MIRT1302469	hsa-miR-3150b-3p	CLIP-seq
MIRT1302451	hsa-miR-3154	CLIP-seq
MIRT2089805	hsa-miR-3165	CLIP-seq
MIRT2610988	hsa-miR-3607-5p	CLIP-seq
MIRT1302452	hsa-miR-3666	CLIP-seq
MIRT2610989	hsa-miR-3668	CLIP-seq
MIRT2610990	hsa-miR-3679-3p	CLIP-seq
MIRT2610991	hsa-miR-3916	CLIP-seq
MIRT2314682	hsa-miR-3973	CLIP-seq
MIRT1302472	hsa-miR-425	CLIP-seq
MIRT2089806	hsa-miR-4259	CLIP-seq
MIRT1302454	hsa-miR-4295	CLIP-seq
MIRT2610992	hsa-miR-4446-5p	CLIP-seq
MIRT2089807	hsa-miR-4456	CLIP-seq
MIRT1302474	hsa-miR-4462	CLIP-seq
MIRT1302476	hsa-miR-4476	CLIP-seq
MIRT1302477	hsa-miR-4496	CLIP-seq
MIRT2610993	hsa-miR-4501	CLIP-seq
MIRT1302455	hsa-miR-4512	CLIP-seq
MIRT2610994	hsa-miR-4527	CLIP-seq
MIRT1302456	hsa-miR-454	CLIP-seq
MIRT2089808	hsa-miR-4639-3p	CLIP-seq
MIRT1302457	hsa-miR-4662a-5p	CLIP-seq
MIRT2610995	hsa-miR-4701-5p	CLIP-seq
MIRT2089809	hsa-miR-4715-3p	CLIP-seq
MIRT2089810	hsa-miR-4715-5p	CLIP-seq
MIRT2610996	hsa-miR-4732-5p	CLIP-seq
MIRT1302490	hsa-miR-4784	CLIP-seq
MIRT2610997	hsa-miR-4793-5p	CLIP-seq
MIRT2610998	hsa-miR-4797-5p	CLIP-seq
MIRT2089811	hsa-miR-509-3p	CLIP-seq
MIRT2314687	hsa-miR-512-5p	CLIP-seq
MIRT2610999	hsa-miR-516b	CLIP-seq
MIRT1302459	hsa-miR-518a-5p	CLIP-seq
MIRT1302460	hsa-miR-519a	CLIP-seq
MIRT1302461	hsa-miR-519b-3p	CLIP-seq
MIRT1302462	hsa-miR-519c-3p	CLIP-seq
MIRT1302463	hsa-miR-527	CLIP-seq
MIRT2611000	hsa-miR-588	CLIP-seq
MIRT1302493	hsa-miR-617	CLIP-seq
MIRT2611001	hsa-miR-626	CLIP-seq
MIRT2611002	hsa-miR-877	CLIP-seq
MIRT2089805	hsa-miR-3165	CLIP-seq
MIRT2610983	hsa-miR-1207-3p	CLIP-seq
MIRT1302443	hsa-miR-1253	CLIP-seq
MIRT2689704	hsa-miR-1257	CLIP-seq
MIRT2089800	hsa-miR-1264	CLIP-seq
MIRT2089801	hsa-miR-128	CLIP-seq
MIRT2689705	hsa-miR-1296	CLIP-seq
MIRT1302444	hsa-miR-130a	CLIP-seq
MIRT1302445	hsa-miR-130b	CLIP-seq
MIRT1302446	hsa-miR-186	CLIP-seq
MIRT1302447	hsa-miR-19a	CLIP-seq
MIRT1302448	hsa-miR-19b	CLIP-seq
MIRT2089802	hsa-miR-203	CLIP-seq
MIRT2610984	hsa-miR-2355-5p	CLIP-seq
MIRT2689706	hsa-miR-2909	CLIP-seq
MIRT1302449	hsa-miR-301a	CLIP-seq
MIRT1302450	hsa-miR-301b	CLIP-seq
MIRT2610986	hsa-miR-3120-5p	CLIP-seq
MIRT2089803	hsa-miR-3128	CLIP-seq
MIRT2089804	hsa-miR-3138	CLIP-seq
MIRT1556988	hsa-miR-3140-3p	CLIP-seq
MIRT1302469	hsa-miR-3150b-3p	CLIP-seq
MIRT1302451	hsa-miR-3154	CLIP-seq
MIRT2689707	hsa-miR-3158-3p	CLIP-seq
MIRT2089805	hsa-miR-3165	CLIP-seq
MIRT2610988	hsa-miR-3607-5p	CLIP-seq
MIRT1302452	hsa-miR-3666	CLIP-seq
MIRT2610990	hsa-miR-3679-3p	CLIP-seq
MIRT1302472	hsa-miR-425	CLIP-seq
MIRT2089806	hsa-miR-4259	CLIP-seq
MIRT1302454	hsa-miR-4295	CLIP-seq
MIRT2689708	hsa-miR-4302	CLIP-seq
MIRT2689709	hsa-miR-4446-3p	CLIP-seq
MIRT2610992	hsa-miR-4446-5p	CLIP-seq
MIRT2089807	hsa-miR-4456	CLIP-seq
MIRT1302474	hsa-miR-4462	CLIP-seq
MIRT1302476	hsa-miR-4476	CLIP-seq
MIRT1302477	hsa-miR-4496	CLIP-seq
MIRT2610993	hsa-miR-4501	CLIP-seq
MIRT1302455	hsa-miR-4512	CLIP-seq
MIRT1302456	hsa-miR-454	CLIP-seq
MIRT2089808	hsa-miR-4639-3p	CLIP-seq
MIRT2689710	hsa-miR-4650-5p	CLIP-seq
MIRT1302457	hsa-miR-4662a-5p	CLIP-seq
MIRT2610995	hsa-miR-4701-5p	CLIP-seq
MIRT2089809	hsa-miR-4715-3p	CLIP-seq
MIRT2089810	hsa-miR-4715-5p	CLIP-seq
MIRT1302490	hsa-miR-4784	CLIP-seq
MIRT2610997	hsa-miR-4793-5p	CLIP-seq
MIRT2610998	hsa-miR-4797-5p	CLIP-seq
MIRT2089811	hsa-miR-509-3p	CLIP-seq
MIRT2314687	hsa-miR-512-5p	CLIP-seq
MIRT1302459	hsa-miR-518a-5p	CLIP-seq
MIRT1302460	hsa-miR-519a	CLIP-seq
MIRT1302461	hsa-miR-519b-3p	CLIP-seq
MIRT1302462	hsa-miR-519c-3p	CLIP-seq
MIRT1302463	hsa-miR-527	CLIP-seq
MIRT2611000	hsa-miR-588	CLIP-seq
MIRT1302493	hsa-miR-617	CLIP-seq
MIRT2611001	hsa-miR-626	CLIP-seq
MIRT2089805	hsa-miR-3165	CLIP-seq

Show/Hide all(23)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000785	Component	Chromatin	ISA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA	9806546
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001221	Function	Transcription coregulator binding	IPI	19041327
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IDA	10586057
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IGI	9806546
GO:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0005515	Function	Protein binding	IPI	10938133, 16464847, 20211142, 20732328, 25752541, 26496610, 28514442, 33961781
GO:0005634	Component	Nucleus	IDA	10938133
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0043565	Function	Sequence-specific DNA binding	IDA	23332764
GO:0045348	Process	Positive regulation of MHC class II biosynthetic process	IDA	19041327
GO:0045348	Process	Positive regulation of MHC class II biosynthetic process	NAS	10938133
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	9806546, 10586057, 10938133, 19041327
GO:0090575	Component	RNA polymerase II transcription regulator complex	IPI	9806546, 10938133
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

MIM	HGNC	e!Ensembl
601863	9986	ENSG00000143390

Protein

UniProt ID

P48382

Protein name

DNA-binding protein RFX5 (Regulatory factor X 5)

Protein function

Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding between RFX and NF-Y. RFX binds the X1 box of MHC-II promoters.

PDB

2KW3 , 3V30

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF18326	RFX5_N	28 → 86	RFX5 N-terminal domain	Domain
PF02257	RFX_DNA_binding	89 → 168	RFX DNA-binding domain	Domain
PF14621	RFX5_DNA_bdg	396 → 614	RFX5 DNA-binding domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous.

Sequence

MAEDEPDAKSPKTGGRAPPGGAEAGEPTTLLQRLRGTISKAVQNKVEGILQDVQKFSDND
KLYLYLQLPSGPTTGDKSSEPSTLSNEEYMYAYRWIRNHLEEHTDTCLPKQSVYDAYRKY
CESLACCRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCYSGIRRKTLVSMPPLPGLDL
KGSESPEMGPEVTPAPRDELVEAACALTCDWAERILKRSFSSIVEVARFLLQQHLISARS
AHAHVLKAMGLAEEDEHAPRERSSKPKNGLENPEGGAHKKPERLAQPPKDLEARTGAGPL
ARGERKKSVVESSAPGANNLQVNALVARLPLLLPRAPRSLIPPIPVSPPILAPRLSSGAL
KVATLPLSSRAGAPPAAVPIINMILPTVPALPGPGPGPGRAPPGGLTQPRGTENREVGIG
GDQGPHDKGVKRTAEVPVSEASGQAPPAKAAKQDIEDTASDAKRKRGRPRKKSGGSGERN
STPLKSAAAMESAQSSRLPWETWGSGGEGNSAGGAERPGPMGEAEKGAVLAQGQGDGTVS
KGGRGPGSQHTKEAEDKIPLVPSKVSVIKGSRSQKEAFPLAKGEVDTAPQGNKDLKEHVL
QSSLSQEHKDPKATPP

Sequence length

616

Interactions

View interactions

	KEGG
	Antigen processing and presentation Tuberculosis Primary immunodeficiency

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Oligodendroglioma	Oligodendroglioma	N/A	N/A	GWAS

Show/Hide Text Mining Associations (13)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Anodontia	Associate	20013806
Bare lymphocyte syndrome 2	Associate	25445815, 9177217
Carcinogenesis	Associate	31188160
Carcinoma Hepatocellular	Associate	31188160, 32883983, 35291486
Carcinoma Non Small Cell Lung	Associate	31096145
Colorectal Neoplasms	Associate	20013806
Genetic Diseases Inborn	Associate	12498778
Malocclusion Angle Class II	Associate	12498778, 16848795, 7744245
Malocclusion Angle Class II	Inhibit	29527204
Neoplasms	Associate	20013806, 36045400
Primary Immunodeficiency Diseases	Associate	20732328
Severe Combined Immunodeficiency	Associate	10825209, 14678199, 7744245, 9177217
Stomach Neoplasms	Associate	32901107, 36045400

RFX5 (regulatory factor X5)