RBKS
protein-codingribokinase
Gene summary
This gene encodes a member of the carbohydrate kinase PfkB family. The encoded protein phosphorylates ribose to form ribose-5-phosphate in the presence of ATP and magnesium as a first step in ribose metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~109.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to RBKS variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022128.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 38 | 1 | 39 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 1 | 0 | 38 | 2 | 0 | 41 |
Highest pathogenic variant AF is 0.00043224037
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071411.1 | 8 | MANE Select | |
| Ensembl | ENSP00000306817.3 | 8 | MANE Select | |
| RefSeq | NP_001274509.1 | 7 | Standard | |
| Ensembl | ENSP00000413789.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Pentose phosphate pathway - Homo sapiens (human)
- Pentose Phosphate Pathway
- Glucose-6-phosphate dehydrogenase deficiency
- Ribose-5-phosphate isomerase deficiency
- Transaldolase deficiency
Biological Process
- pentose-phosphate shunt
- D-ribose catabolic process
- carbohydrate phosphorylation
Molecular Function
- ribokinase activity
- protein binding
- ATP binding
- metal ion binding
Cellular Component
- nucleus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000302188
- Coding exons
- 8
- Length
- 109735
- Individuals with no LoFs
- 123635
- Homozygous LoFs
- 17
- Heterozygous LoFs
- 2096
- Defined
- 125748
- p
- 0.00844
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.252 | 161 | 170 | 0.946 | 0.00000816 | 2071 |
| Missense (PolyPhen) | 58 | 63.176 | 0.91807 | 755 | ||
| Synonymous | 0.811 | 56 | 64.3 | 0.871 | 0.00000326 | 649 |
| Loss of Function | 0.114 | 13 | 13.5 | 0.966 | 5.65e-7 | 180 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0020 | 0.0020 | notable |
| Latino/Admixed American | 0.0020 | 0.0019 | notable |
| Ashkenazi Jewish | 0.0097 | 0.0094 | notable |
| East Asian | 0.015 | 0.014 | notable |
| Finnish | 0.0085 | 0.0083 | notable |
| European (Non-Finnish) | 0.011 | 0.010 | notable |
| South Asian | 0.0089 | 0.0088 | notable |
| Other | 0.0088 | 0.0083 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5- phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway. {ECO:0000255|HAMAP-Rule:MF_03215, ECO:0000269|PubMed:17585908}.;
Intolerance Scores
- LoFtool
- 0.824
- RVIS EVS
- 0.15
- RVIS percentile EVS
- 64.61
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.528
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |