NTAN1

N-terminal asparagine amidase

Basic information

Region (hg38): 16:15037853-15056079

Links

ENSG00000157045 ∙ NCBI:123803 ∙ OMIM:615367 ∙ HGNC:29909 ∙ Uniprot:Q96AB6 ∙ 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 NTAN1 gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NTAN1 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in NTAN1

This is a list of pathogenic ClinVar variants found in the NTAN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-15038059-C-G		not specified	Uncertain significance (Dec 01, 2022)
16-15038152-G-T		not specified	Uncertain significance (Feb 05, 2024)
16-15038153-T-C		not specified	Uncertain significance (Mar 22, 2023)
16-15038197-G-A		not specified	Uncertain significance (Dec 13, 2022)
16-15038650-C-T		not specified	Uncertain significance (Dec 21, 2022)
16-15038668-G-A		not specified	Uncertain significance (Jul 15, 2021)
16-15039970-G-C		not specified	Uncertain significance (May 10, 2022)
16-15039998-G-T		not specified	Uncertain significance (Dec 17, 2023)
16-15041109-C-T		not specified	Uncertain significance (Feb 05, 2024)
16-15041111-G-C		not specified	Uncertain significance (Nov 09, 2021)
16-15047449-A-G		not specified	Uncertain significance (Jan 23, 2024)
16-15047475-A-G		not specified	Uncertain significance (Jun 09, 2022)
16-15047518-C-T		not specified	Uncertain significance (Dec 08, 2023)
16-15047873-C-T		not specified	Uncertain significance (Jun 02, 2023)
16-15048031-C-A			Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTAN1	protein_coding	protein_coding	ENST00000287706	10	18212

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000273	0.771	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.403	143	157	0.910	0.00000809	2003
Missense in Polyphen		37	43.878	0.84326		527
Synonymous	-0.433	62	57.8	1.07	0.00000332	607
Loss of Function	1.25	11	16.5	0.667	7.82e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000304
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: N-terminal asparagine deamidase that mediates deamidation of N-terminal asparagine residues to aspartate. Required for the ubiquitin-dependent turnover of intracellular proteins that initiate with Met-Asn. These proteins are acetylated on the retained initiator methionine and can subsequently be modified by the removal of N-acetyl methionine by acylaminoacid hydrolase (AAH). Conversion of the resulting N-terminal asparagine to aspartate by NTAN1/PNAD renders the protein susceptible to arginylation, polyubiquitination and degradation as specified by the N-end rule. This enzyme does not act on substrates with internal or C-terminal asparagines and does not act on glutamine residues in any position, nor on acetylated N-terminal peptidyl Asn. {ECO:0000269|PubMed:21375249}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.680
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.202
• hipred: N
• hipred_score: 0.394
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.358

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ntan1
• Phenotype: growth/size/body region phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;memory;adult locomotory behavior
• Cellular component: nucleus;cytoplasm
• Molecular function: protein-N-terminal asparagine amidohydrolase activity