RFX5
Basic information
Region (hg38): 1:151340640-151347326
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
MHC class II deficiency 3; MHC class II deficiency 5 | AR | Allergy/Immunology/Infectious | Prophylaxis and early and aggressive treatment of infections can be beneficial; BMT has been reported in Bare lymphocyte syndrome, type II | Allergy/Immunology/Infectious; Gastrointestinal | 7744245; 9401005; 10079298; 12368908 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 73 | 78 | ||||
missense | 206 | 218 | ||||
nonsense | 12 | |||||
start loss | 0 | |||||
frameshift | 13 | 25 | ||||
splice donor/acceptor (+/-2bp) | 10 | 13 | ||||
Total | 25 | 20 | 213 | 82 | 6 |
Highest pathogenic variant AF is 0.000180714
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RFX5 | protein_coding | protein_coding | ENST00000290524 | 9 | 6718 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.96e-11 | 0.391 | 125682 | 0 | 66 | 125748 | 0.000262 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.476 | 314 | 339 | 0.927 | 0.0000198 | 3915 |
Missense in Polyphen | 92 | 111.4 | 0.82589 | 1248 | ||
Synonymous | 2.23 | 95 | 127 | 0.748 | 0.00000661 | 1348 |
Loss of Function | 1.14 | 20 | 26.3 | 0.760 | 0.00000183 | 299 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000669 | 0.000662 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000218 | 0.000217 |
Finnish | 0.00111 | 0.00111 |
European (Non-Finnish) | 0.000150 | 0.000149 |
Middle Eastern | 0.000218 | 0.000217 |
South Asian | 0.000196 | 0.000196 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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