FRK
protein-codingfyn related Src family tyrosine kinase, the group of Src family tyrosine kinases|SH2 domain containing
Gene summary
The protein encoded by this gene belongs to the TYR family of protein kinases. This tyrosine kinase is a nuclear protein and may function during G1 and S phase of the cell cycle and suppress growth. [provided by RefSeq, Jul 2008]
- PTK5
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~129.7 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 FRK variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002031.3. 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 | 1 | 1 | 2 | |||
| missense | 41 | 2 | 43 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 45 | 3 | 0 | 48 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002022.1 | 8 | MANE Select | |
| Ensembl | ENSP00000476145.1 | 8 | MANE Select | |
| Ensembl | ENSP00000561285.1 | 8 | Standard | |
| Ensembl | ENSP00000561285.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neutrophil degranulation
- Signal Transduction
- Regulation of PTEN stability and activity
- Innate Immune System
- Immune System
Biological Process
- negative regulation of transcription by RNA polymerase II
- protein phosphorylation
- transmembrane receptor protein tyrosine kinase signaling pathway
- negative regulation of cell population proliferation
- cell differentiation
Molecular Function
- protein tyrosine kinase activity
- non-membrane spanning protein tyrosine kinase activity
- signaling receptor binding
- protein binding
- ATP binding
Cellular Component
- extracellular region
- nucleus
- cytosol
- extrinsic component of cytoplasmic side of plasma membrane
- azurophil granule lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000606080
- Coding exons
- 8
- Length
- 129610
- Individuals with no LoFs
- 125627
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 120
- Defined
- 125748
- p
- 0.000481
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.686 | 239 | 271 | 0.883 | 0.0000141 | 3304 |
| Missense (PolyPhen) | 78 | 114.77 | 0.67964 | 1361 | ||
| Synonymous | -0.857 | 114 | 103 | 1.11 | 0.00000594 | 937 |
| Loss of Function | 1.20 | 22 | 29.0 | 0.759 | 0.00000178 | 306 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00074 | 0.00074 | rare |
| Latino/Admixed American | 0.00030 | 0.00029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00042 | 0.00040 | rare |
| South Asian | 0.0014 | 0.0014 | notable |
| Other | 0.00066 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Non-receptor tyrosine-protein kinase that negatively regulates cell proliferation. Positively regulates PTEN protein stability through phosphorylation of PTEN on 'Tyr-336', which in turn prevents its ubiquitination and degradation, possibly by reducing its binding to NEDD4. May function as a tumor suppressor. {ECO:0000269|PubMed:19345329}.;
Recessive Scores
- pRec
- 0.170
Intolerance Scores
- LoFtool
- 0.458
- RVIS EVS
- -0.33
- RVIS percentile EVS
- 30.74
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.951
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |