NIFK
protein-codingnucleolar protein interacting with the FHA domain of MKI67, the group of RNA binding motif containing
Gene summary
This gene encodes a protein that interacts with the forkhead-associated domain of the Ki-67 antigen. The encoded protein may bind RNA and may play a role in mitosis and cell cycle progression. Multiple pseudogenes exist on chromosomes 5, 10, 12, 15, and 19.[provided by RefSeq, Jan 2009]
- MKI67IP
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~10.0 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 NIFK variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032390.5. 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 | 34 | 2 | 36 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 34 | 3 | 0 | 37 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_115766.3 | 7 | MANE Select | |
| Ensembl | ENSP00000285814.4 | 7 | MANE Select | |
| Ensembl | ENSP00000390174.1 | 3 | Standard | |
| Ensembl | ENSP00000406227.1 | 5 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| nifk | Danio rerio | Structure: trunk Quality: necrotic abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- rRNA transcription
- rRNA metabolic process
- protein-containing complex assembly
Molecular Function
- RNA binding
- protein binding
Cellular Component
- condensed nuclear chromosome
- nucleoplasm
- nucleolus
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000285814
- Coding exons
- 7
- Length
- 9979
- Individuals with no LoFs
- 125528
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 216
- Defined
- 125744
- p
- 0.000859
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.567 | 181 | 161 | 1.13 | 0.00000878 | 1906 |
| Missense (PolyPhen) | 26 | 27.239 | 0.9545 | 354 | ||
| Synonymous | -0.824 | 64 | 56.1 | 1.14 | 0.00000267 | 550 |
| Loss of Function | 1.69 | 8 | 15.1 | 0.530 | 8.05e-7 | 185 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00018 | 0.00017 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.0036 | 0.0036 | notable |
| European (Non-Finnish) | 0.0011 | 0.0011 | notable |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00066 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0942
Intolerance Scores
- RVIS EVS
- -0.32
- RVIS percentile EVS
- 31.69
Essentials
- Essential (gene trap)
- E
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |