NIT2
protein-codingnitrilase family member 2
Gene summary
Enables omega-amidase activity. Involved in L-glutamine metabolic process; asparagine metabolic process; and oxaloacetate metabolic process. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~26.9 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 NIT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020202.5. 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 | 37 | 1 | 38 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 42 | 1 | 0 | 43 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_064587.1 | 10 | MANE Select | |
| Ensembl | ENSP00000377696.3 | 10 | MANE Select | |
| Ensembl | ENSP00000419239.1 | 1 | Standard | |
| Ensembl | ENSP00000419157.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Alanine, aspartate and glutamate metabolism - Homo sapiens (human)
- Neutrophil degranulation
- Innate Immune System
- Immune System
Biological Process
- oxaloacetate metabolic process
- asparagine metabolic process
- glutamine metabolic process
- neutrophil degranulation
Molecular Function
- omega-amidase activity
Cellular Component
- extracellular region
- centrosome
- cytosol
- specific granule lumen
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000394140
- Coding exons
- 10
- Length
- 22166
- Individuals with no LoFs
- 125697
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 51
- Defined
- 125748
- p
- 0.000203
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.401 | 146 | 160 | 0.911 | 0.00000923 | 1775 |
| Missense (PolyPhen) | 44 | 47.398 | 0.9283 | 514 | ||
| Synonymous | -0.591 | 63 | 57.3 | 1.10 | 0.00000326 | 533 |
| Loss of Function | -1.09 | 23 | 18.0 | 1.28 | 9.38e-7 | 215 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00035 | 0.00035 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00021 | 0.00021 | rare |
| South Asian | 0.00033 | 0.00033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Has a omega-amidase activity. The role of omega-amidase is to remove potentially toxic intermediates by converting alpha- ketoglutaramate and alpha-ketosuccinamate to biologically useful alpha-ketoglutarate and oxaloacetate, respectively. Overexpression decreases the colony-forming capacity of cultured cells by arresting cells in the G2 phase of the cell cycle. {ECO:0000269|PubMed:17488281, ECO:0000269|PubMed:19595734}.;
Recessive Scores
- pRec
- 0.193
Intolerance Scores
- LoFtool
- 0.437
- RVIS EVS
- -0.8
- RVIS percentile EVS
- 12.24
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.159
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |