FN3KRP
protein-codingfructosamine 3 kinase related protein
Gene summary
A high concentration of glucose can result in non-enzymatic oxidation of proteins by reaction of glucose and lysine residues (glycation). Proteins modified in this way are less active or functional. This gene encodes an enzyme which catalyzes the phosphorylation of psicosamines and ribulosamines compared to the neighboring gene which encodes a highly similar enzyme, fructosamine-3-kinase, which has different substrate specificity. The activity of both enzymes may result in deglycation of proteins to restore their function. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.6 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 FN3KRP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024619.4. 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 | 3 | 3 | ||||
| missense | 80 | 4 | 84 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 85 | 4 | 0 | 89 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_078895.2 | 6 | MANE Select | |
| Ensembl | ENSP00000269373.6 | 6 | MANE Select | |
| Ensembl | ENSP00000459751.1 | 2 | Standard | |
| Ensembl | ENSP00000460243.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Post-translational protein modification
- Metabolism of proteins
- Gamma carboxylation, hypusine formation and arylsulfatase activation
Biological Process
- phosphorylation
- post-translational protein modification
Molecular Function
- kinase activity
Cellular Component
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000269373
- Coding exons
- 6
- Length
- 13646
- Individuals with no LoFs
- 125553
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 193
- Defined
- 125748
- p
- 0.000776
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.330 | 199 | 186 | 1.07 | 0.0000106 | 2008 |
| Missense (PolyPhen) | 82 | 84.743 | 0.96763 | 953 | ||
| Synonymous | -0.636 | 81 | 74.0 | 1.09 | 0.00000452 | 590 |
| Loss of Function | 0.0774 | 13 | 13.3 | 0.977 | 5.72e-7 | 159 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00055 | 0.00055 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00040 | 0.00037 | rare |
| European (Non-Finnish) | 0.00033 | 0.00033 | rare |
| South Asian | 0.0043 | 0.0043 | notable |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Phosphorylates psicosamines and ribulosamines, but not fructosamines, on the third carbon of the sugar moiety. Protein- bound psicosamine 3-phosphates and ribulosamine 3-phosphates are unstable and decompose under physiological conditions. Thus phosphorylation leads to deglycation. {ECO:0000269|PubMed:14633848, ECO:0000269|PubMed:15137908}.;
Intolerance Scores
- LoFtool
- 0.854
- RVIS EVS
- 0.02
- RVIS percentile EVS
- 55.61
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.778
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |