GeneBe

RFX5

regulatory factor X5, the group of Regulatory factor X family

Basic information

Region (hg38): 1:151340640-151347326

Links

ENSG00000143390 ∙ NCBI:5993 ∙ OMIM:601863 ∙ HGNC:9986 ∙ Uniprot:P48382 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • MHC class II deficiency (Supportive), mode of inheritance: AR
  • MHC class II deficiency (Strong), mode of inheritance: AR
  • MHC class II deficiency (Definitive), mode of inheritance: AR
  • MHC class II deficiency (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
MHC class II deficiency 3; MHC class II deficiency 5ARAllergy/Immunology/InfectiousProphylaxis and early and aggressive treatment of infections can be beneficial; BMT has been reported in Bare lymphocyte syndrome, type IIAllergy/Immunology/Infectious; Gastrointestinal7744245; 9401005; 10079298; 12368908

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RFX5 gene.

  • MHC_class_II_deficiency (358 variants)
  • not_specified (89 variants)
  • not_provided (22 variants)
  • MHC_class_II_deficiency_3 (12 variants)
  • RFX5-related_disorder (11 variants)
  • MHC_class_II_deficiency_5 (4 variants)
  • MHC_class_II_deficiency_1 (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFX5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001025603.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
73
clinvar
4
clinvar
 78
missense
1
clinvar
206
clinvar
9
clinvar
2
clinvar
 218
nonsense
9
clinvar
2
clinvar
1
clinvar
 12
start loss
0
frameshift
13
clinvar
7
clinvar
5
clinvar
 25
splice donor/acceptor (+/-2bp)
3
clinvar
10
clinvar
 13
Total 25 20 213 82 6

Highest pathogenic variant AF is 0.000180714

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RFX5protein_codingprotein_codingENST00000290524 96718
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.96e-110.3911256820661257480.000262
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4763143390.9270.00001983915
Missense in Polyphen92111.40.825891248
Synonymous2.23951270.7480.000006611348
Loss of Function1.142026.30.7600.00000183299

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006690.000662
Ashkenazi Jewish0.000.00
East Asian0.0002180.000217
Finnish0.001110.00111
European (Non-Finnish)0.0001500.000149
Middle Eastern0.0002180.000217
South Asian0.0001960.000196
Other0.000.00

dbNSFP

Source: dbNSFP

Function
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.;
Disease
DISEASE: Bare lymphocyte syndrome 2 (BLS2) [MIM:209920]: A severe combined immunodeficiency disease with early onset. It is characterized by a profound defect in constitutive and interferon- gamma induced MHC II expression, absence of cellular and humoral T-cell response to antigen challenge, hypogammaglobulinemia and impaired antibody production. The consequence include extreme susceptibility to viral, bacterial and fungal infections. {ECO:0000269|PubMed:10825209}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Antigen processing and presentation - Homo sapiens (human);Primary immunodeficiency - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Prion disease pathway (Consensus)

Recessive Scores

pRec
0.137

Intolerance Scores

loftool
0.506
rvis_EVS
0.04
rvis_percentile_EVS
57.41

Haploinsufficiency Scores

pHI
0.131
hipred
N
hipred_score
0.377
ghis
0.569

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
1.00

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rfx5
Phenotype
endocrine/exocrine gland phenotype; immune system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype;

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II
Cellular component
nucleus
Molecular function
RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding