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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	8625
Gene name	Regulatory factor X associated ankyrin containing protein
Gene symbol	RFXANK
Synonyms (NCBI Gene)	ANKRA1BLSF14150_1MHC2D2RFX-B
Chromosome	19
Chromosome location	19p13.11
Summary	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 protein and regulatory facto

Show/Hide all (8)

SNP ID	Visualize variation	Clinical significance	Consequence
rs104894709	A>T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs751386365	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs753338285	AT>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs759667201	G>A,C	Pathogenic	Splice donor variant
rs869312922	G>T	Pathogenic	Splice donor variant
rs1568578781	->CTGCC	Pathogenic	Splice donor variant
rs1568579997	TTCGCTTCCTGCTGGAGTGGGTGCGTCCCAGCCCAGCTGGGCAGCTGGGGGGTTCCCG>-	Likely-pathogenic	Intron variant, coding sequence variant, splice donor variant
rs1599784374	T>A	Likely-pathogenic	Coding sequence variant, stop gained

Show/Hide all (32)

miRTarBase ID	miRNA	Experiments	Reference
MIRT439777	hsa-miR-106b-5p	HITS-CLIP	22473208
MIRT439776	hsa-miR-20a-5p	HITS-CLIP	22473208
MIRT439777	hsa-miR-106b-5p	HITS-CLIP	22473208
MIRT726753	hsa-miR-17-5p	HITS-CLIP	22473208
MIRT726752	hsa-miR-20b-5p	HITS-CLIP	22473208
MIRT726751	hsa-miR-93-5p	HITS-CLIP	22473208
MIRT726750	hsa-miR-519d-3p	HITS-CLIP	22473208
MIRT439776	hsa-miR-20a-5p	HITS-CLIP	22473208
MIRT1302629	hsa-miR-125a-5p	CLIP-seq
MIRT1302630	hsa-miR-125b	CLIP-seq
MIRT1302631	hsa-miR-149	CLIP-seq
MIRT1302632	hsa-miR-223	CLIP-seq
MIRT1302633	hsa-miR-2355-5p	CLIP-seq
MIRT1302634	hsa-miR-3064-5p	CLIP-seq
MIRT1302635	hsa-miR-3616-5p	CLIP-seq
MIRT1302636	hsa-miR-3647-5p	CLIP-seq
MIRT1302637	hsa-miR-3659	CLIP-seq
MIRT1302638	hsa-miR-3679-3p	CLIP-seq
MIRT1302639	hsa-miR-375	CLIP-seq
MIRT1302640	hsa-miR-4267	CLIP-seq
MIRT1302641	hsa-miR-4277	CLIP-seq
MIRT1302642	hsa-miR-4314	CLIP-seq
MIRT1302643	hsa-miR-4319	CLIP-seq
MIRT1302644	hsa-miR-4658	CLIP-seq
MIRT1302645	hsa-miR-4682	CLIP-seq
MIRT1302646	hsa-miR-4732-3p	CLIP-seq
MIRT1302647	hsa-miR-4794	CLIP-seq
MIRT1302648	hsa-miR-573	CLIP-seq
MIRT1302649	hsa-miR-574-5p	CLIP-seq
MIRT1302650	hsa-miR-591	CLIP-seq
MIRT1302651	hsa-miR-629	CLIP-seq
MIRT1302652	hsa-miR-670	CLIP-seq

Show/Hide all (18)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA	9806546
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IDA	9806546
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	10938133, 20211142, 25752541, 31864703, 33961781
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	10938133
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA
GO:0007265	Process	Ras protein signal transduction	IEA
GO:0042826	Function	Histone deacetylase binding	IEA
GO:0045171	Component	Intercellular bridge	IDA
GO:0045348	Process	Positive regulation of MHC class II biosynthetic process	NAS	10938133
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IBA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	9806546, 10938133
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0090575	Component	RNA polymerase II transcription regulator complex	IPI	9806546, 10938133

MIM	HGNC	e!Ensembl
603200	9987	ENSG00000064490

O14593

Protein name

DNA-binding protein RFXANK (Ankyrin repeat family A protein 1) (Regulatory factor X subunit B) (RFX-B) (Regulatory factor X-associated ankyrin-containing protein)

Protein function

Activates transcription from class II MHC promoters. Activation requires the activity of the MHC class II transactivator/CIITA. May regulate other genes in the cell. RFX binds the X1 box of MHC-II promoters (PubMed:10072068, PubMed:10725724, Pub

PDB

3UXG , 3V30 , 6MEW

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00023	Ank	123 → 155	Ankyrin repeat	Repeat
PF00023	Ank	189 → 221	Ankyrin repeat	Repeat

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous.

Sequence

MELTQPAEDLIQTQQTPASELGDPEDPGEEAADGSDTVVLSLFPCTPEPVNPEPDASVSS
PQAGSSLKHSTTLTNRQRGNEVSALPATLDSLSIHQLAAQGELDQLKEHLRKGDNLVNKP
DERGFTPLIWASAFGEIETVRFLLEWGADPHILAKERESALSLASTGGYTDIVGLLLERD
VDINIYDWNGGTPLLYAVRGNHVKCVEALLARGADLTTEADSGYTPMDLAVALGYRKVQQ
VIENHILKLFQSNLVPADPE

Sequence length

260

Interactions

View interactions

	KEGG
	Antigen processing and presentation Tuberculosis Primary immunodeficiency

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Inherited Immunodeficiency Diseases	Likely pathogenic	rs751386365	RCV001027618	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MHC class II deficiency	Likely pathogenic; Pathogenic	rs1568579235, rs770387882, rs747402973, rs2146483253, rs2146496053, rs2146493181, rs776752313, rs2146492780, rs759667201, rs104894709, rs1599784393, rs1568578781, rs778357787, rs1599784374, rs1568579997 View all (5 more)	RCV001379137 RCV001385858 RCV001388116 RCV002028777 RCV001932009 View all (16 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MHC class II deficiency 1	Pathogenic; Likely pathogenic	rs776752313, rs104894709	RCV004558747 RCV005630244	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MHC class II deficiency 2	Likely pathogenic; Pathogenic	rs1568579235, rs747402973, rs776752313, rs759667201, rs104894709, rs2512793715, rs1568579997, rs753338285, rs751386365, rs779699696	RCV005023128 RCV004576989 RCV004577006 RCV004576879 RCV004576880 View all (5 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MHC class II deficiency 3	Likely pathogenic; Pathogenic	rs759667201	RCV004018579	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
RFXANK-related disorder	Likely pathogenic	rs2512813276, rs1568579997	RCV003400460 RCV003411751	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Thyroid cancer, nonmedullary, 1	Likely pathogenic; Pathogenic	rs779699696	RCV005912507	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (16)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Acute myeloid leukemia	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BARE LYMPHOCYTE SYNDROME 2	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BARE LYMPHOCYTE SYNDROME, TYPE II, COMPLEMENTATION GROUP A	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign; Likely benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Likely benign; Benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MHC class II deficiency 5	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SEVERE COMBINED IMMUNODEFICIENCY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (36)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Acute otitis media	Otitis media	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Adenocarcinoma	Adenocarcinoma	BEFREE	11836625		★★★★★ ★☆☆☆☆ Found in Text Mining only
Agammaglobulinemia	Agammaglobulinemia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Autoimmune hemolytic anemia	Autoimmune hemolytic anemia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Bare Lymphocyte Syndrome	Bare Lymphocyte Syndrome	BEFREE	10072068, 15655668		★★★★★ ★☆☆☆☆ Found in Text Mining only
Bare lymphocyte syndrome 2	Bare Lymphocyte Syndrome	BEFREE	10072068, 10825209, 15655668		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bare lymphocyte syndrome 2	Bare Lymphocyte Syndrome	UNIPROT_DG	10072068, 10725724, 22649097, 9806546		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bare lymphocyte syndrome 2	Bare lymphocyte syndrome	Pubtator	35065305	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bare lymphocyte syndrome 2	Bare Lymphocyte Syndrome	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bare lymphocyte syndrome 2	Bare Lymphocyte Syndrome	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bare lymphocyte syndrome 2	Bare Lymphocyte Syndrome	ORPHANET_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bare Lymphocyte Syndrome, Type II, Complementation Group B	Bare Lymphocyte Syndrome	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cholangitis	Cholangitis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cholangitis, Sclerosing	Cholangitis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Chronic kidney disease stage 5	Kidney Disease	BEFREE	27943170		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colitis	Colitis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal Neoplasms	LHGDN	11836625		★★★★★ ★☆☆☆☆ Found in Text Mining only
Combined immunodeficiency	Severe combined immunodeficiency disease	BEFREE	14574520, 21908431		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diffuse Large B-Cell Lymphoma	Diffuse Lymphoma	BEFREE	21166693		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Encephalitis	Encephalitis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Enteritis	Enteritis	BEFREE	27881419		★★★★★ ★☆☆☆☆ Found in Text Mining only
Immune thrombocytopenic purpura	Immune Thrombocytopenic Purpura	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Immunodeficiency by defective expression of MHC class II	Bare Lymphocyte Syndrome	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Failure, Chronic	Kidney Failure	BEFREE	27943170		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malabsorption Syndrome	Malabsorption Syndrome	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	11836625		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	11836625		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neutropenia	Neutropenia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancytopenia	Pancytopenia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Patent ductus arteriosus	Patent ductus arteriosus	BEFREE	28232519		★★★★★ ★☆☆☆☆ Found in Text Mining only
Reticulosarcoma	Reticulosarcoma	BEFREE	21166693		★★★★★ ★☆☆☆☆ Found in Text Mining only
Rhinitis	Rhinitis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Severe Combined Immunodeficiency	Severe combined immunodeficiency	Pubtator	10072068, 10725724, 10825209, 38441205	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sinusitis	Sinusitis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Transitional cell carcinoma of bladder	Bladder carcinoma	BEFREE	16953298		★★★★★ ★☆☆☆☆ Found in Text Mining only

RFXANK (regulatory factor X associated ankyrin containing protein)