RFK
Basic information
Region (hg38): 9:76385526-76394517
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (13 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFK gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018339.6. 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 | 0 | |||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RFK | protein_coding | protein_coding | ENST00000376736 | 4 | 9001 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0639 | 0.877 | 125741 | 0 | 5 | 125746 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.493 | 69 | 81.5 | 0.846 | 0.00000364 | 1021 |
| Missense in Polyphen | 16 | 22.968 | 0.69661 | 315 | ||
| Synonymous | -0.533 | 32 | 28.4 | 1.13 | 0.00000129 | 280 |
| Loss of Function | 1.59 | 3 | 7.78 | 0.386 | 4.26e-7 | 91 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000294 | 0.0000294 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000114 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.000114 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the phosphorylation of riboflavin (vitamin B2) to form flavin-mononucleotide (FMN), hence rate-limiting enzyme in the synthesis of FAD. Essential for TNF-induced reactive oxygen species (ROS) production. Through its interaction with both TNFRSF1A and CYBA, physically and functionally couples TNFRSF1A to NADPH oxidase. TNF-activation of RFK may enhance the incorporation of FAD in NADPH oxidase, a critical step for the assembly and activation of NADPH oxidase. {ECO:0000269|PubMed:19641494}.;
- Pathway
- Riboflavin metabolism - Homo sapiens (human);Riboflavin Metabolism;Selenium Micronutrient Network;Folate Metabolism;TNF alpha Signaling Pathway;Metabolism;Vitamin B2 (riboflavin) metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;flavin biosynthesis;TNFalpha
(Consensus)
Recessive Scores
- pRec
- 0.153
Intolerance Scores
- loftool
- 0.182
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.0665
- hipred
- N
- hipred_score
- 0.332
- ghis
- 0.602
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.396
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rfk
- Phenotype
- homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- riboflavin metabolic process;apoptotic process;riboflavin biosynthetic process;FMN biosynthetic process;phosphorylation;positive regulation of NAD(P)H oxidase activity;reactive oxygen species metabolic process
- Cellular component
- cytoplasm;cytosol
- Molecular function
- protein binding;ATP binding;riboflavin kinase activity;metal ion binding