NIT2

nitrilase family member 2

Basic information

Region (hg38): 3:100334739-100361635

Links

ENSG00000114021

∙ NCBI:56954 ∙ OMIM:616769 ∙ HGNC:29878 ∙ Uniprot:Q9NQR4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NIT2 gene.

not_specified (28 variants)

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. These statistics are base on transcript: NM_000020202.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			32 clinvar	1 clinvar		33
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	37	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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