NIT1

nitrilase 1

Basic information

Region (hg38): 1:161118086-161125445

Links

ENSG00000158793 ∙ NCBI:4817 ∙ OMIM:604618 ∙ HGNC:7828 ∙ Uniprot:Q86X76 ∙ 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 NIT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIT1 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			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding			15			15
Total	0	1	51	1	0

Variants in NIT1

This is a list of pathogenic ClinVar variants found in the NIT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-161118850-C-T		not specified	Uncertain significance (Dec 13, 2023)
1-161118856-C-T		not specified	Uncertain significance (Nov 09, 2024)
1-161118865-C-T		not specified	Uncertain significance (Jun 08, 2022)
1-161118878-C-T		not specified	Uncertain significance (Nov 22, 2021)
1-161119138-A-G		not specified	Uncertain significance (Dec 03, 2024)
1-161119146-G-A		not specified	Uncertain significance (Apr 07, 2023)
1-161119168-G-A		not specified	Likely benign (Aug 20, 2024)
1-161119186-G-A		not specified	Uncertain significance (Dec 31, 2024)
1-161119189-T-A		not specified	Uncertain significance (Feb 14, 2023)
1-161119238-C-T		not specified	Uncertain significance (Feb 28, 2025)
1-161119250-G-A		not specified	Uncertain significance (Jun 18, 2021)
1-161119253-A-G		not specified	Uncertain significance (Jul 30, 2024)
1-161119255-G-C		not specified	Uncertain significance (May 26, 2022)
1-161119271-C-G		not specified	Uncertain significance (Oct 20, 2024)
1-161119328-C-T		not specified	Uncertain significance (Mar 20, 2023)
1-161119384-G-A		not specified	Uncertain significance (May 10, 2024)
1-161119519-C-T		not specified	Uncertain significance (Mar 06, 2025)
1-161119861-T-G		not specified	Uncertain significance (Dec 27, 2023)
1-161119869-C-T		not specified	Uncertain significance (Sep 07, 2022)
1-161119890-G-C		not specified	Uncertain significance (Apr 08, 2023)
1-161119897-A-G		not specified	Uncertain significance (Apr 04, 2024)
1-161119900-C-T		not specified	Uncertain significance (Jul 10, 2024)
1-161119909-C-T		not specified	Uncertain significance (May 17, 2023)
1-161119954-T-G		Susceptibility to severe COVID-19	Likely pathogenic (Jul 22, 2024)
1-161120113-C-A		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIT1	protein_coding	protein_coding	ENST00000368009	7	7360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.94e-7	0.770	125648	0	100	125748	0.000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.598	217	194	1.12	0.0000107	2086
Missense in Polyphen		57	57.244	0.99574		573
Synonymous	-0.426	76	71.4	1.06	0.00000346	712
Loss of Function	1.30	12	17.9	0.670	0.00000106	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00105	0.00105
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000450	0.000448
Middle Eastern	0.000381	0.000381
South Asian	0.000327	0.000327
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the hydrolysis of the amide bond in N-(4- oxoglutarate)-L-cysteinylglycine (deaminated glutathione), a metabolite repair reaction to dispose of the harmful deaminated glutathione. Plays a role in cell growth and apoptosis: loss of expression promotes cell growth, resistance to DNA damage stress and increased incidence to NMBA-induced tumors. Has tumor suppressor properties that enhances the apoptotic responsiveness in cancer cells; this effect is additive to the tumor suppressor activity of FHIT. It is also a negative regulator of primary T- cells. {ECO:0000250|UniProtKB:Q8VDK1}.

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.137
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.252
• hipred: N
• hipred_score: 0.196
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.261

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nit1
• Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; neoplasm; normal phenotype

Gene ontology

• Biological process: nitrogen compound metabolic process;biological_process
• Cellular component: nucleus;mitochondrion
• Molecular function: nitrilase activity;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides