NIT2
Basic information
Region (hg38): 3:100334739-100361635
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIT2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 13 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 1 | 0 |
Variants in NIT2
This is a list of pathogenic ClinVar variants found in the NIT2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-100334795-A-G | not specified | Likely benign (Jun 09, 2022) | ||
| 3-100339125-A-G | not specified | Uncertain significance (Apr 28, 2022) | ||
| 3-100339146-C-T | not specified | Uncertain significance (Jan 16, 2024) | ||
| 3-100339164-C-T | not specified | Uncertain significance (Jan 16, 2024) | ||
| 3-100339819-G-A | not specified | Uncertain significance (Sep 25, 2024) | ||
| 3-100339840-C-T | not specified | Uncertain significance (Jan 30, 2025) | ||
| 3-100341075-T-G | not specified | Uncertain significance (Nov 07, 2022) | ||
| 3-100345606-G-A | not specified | Uncertain significance (May 31, 2023) | ||
| 3-100345631-A-G | not specified | Uncertain significance (Jan 08, 2025) | ||
| 3-100345649-C-T | not specified | Uncertain significance (Oct 04, 2022) | ||
| 3-100346217-T-C | not specified | Uncertain significance (Dec 21, 2022) | ||
| 3-100348806-G-T | not specified | Uncertain significance (Feb 17, 2023) | ||
| 3-100348880-C-T | not specified | Uncertain significance (Jun 22, 2024) | ||
| 3-100355200-C-T | not specified | Uncertain significance (Jun 07, 2023) | ||
| 3-100355216-T-C | not specified | Uncertain significance (Jan 04, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NIT2 | protein_coding | protein_coding | ENST00000394140 | 10 | 22166 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.15e-17 | 0.000727 | 125697 | 0 | 51 | 125748 | 0.000203 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.401 | 146 | 160 | 0.911 | 0.00000923 | 1775 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000540 | 0.000532 |
| Ashkenazi Jewish | 0.0000994 | 0.0000992 |
| East Asian | 0.0000546 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000212 | 0.000211 |
| Middle Eastern | 0.0000546 | 0.0000544 |
| South Asian | 0.000327 | 0.000327 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- Alanine, aspartate and glutamate metabolism - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.193
Intolerance Scores
- loftool
- 0.437
- rvis_EVS
- -0.8
- rvis_percentile_EVS
- 12.24
Haploinsufficiency Scores
- pHI
- 0.0899
- hipred
- N
- hipred_score
- 0.466
- ghis
- 0.631
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.159
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nit2
- Phenotype
Gene ontology
- Biological process
- oxaloacetate metabolic process;asparagine metabolic process;glutamine metabolic process;neutrophil degranulation
- Cellular component
- extracellular region;centrosome;cytosol;specific granule lumen;extracellular exosome;tertiary granule lumen
- Molecular function
- omega-amidase activity