NUDT16L1

nudix hydrolase 16 like 1, the group of Nudix hydrolase family

Basic information

Region (hg38): 16:4693562-4695859

Links

ENSG00000168101 ∙ NCBI:84309 ∙ OMIM:617338 ∙ HGNC:28154 ∙ Uniprot:Q9BRJ7 ∙ 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 NUDT16L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT16L1 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				3		3
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	0

Variants in NUDT16L1

This is a list of pathogenic ClinVar variants found in the NUDT16L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-4693746-C-T		not specified	Uncertain significance (Dec 12, 2024)
16-4693759-G-T		not specified	Uncertain significance (Oct 19, 2024)
16-4693763-A-G		not specified	Uncertain significance (Apr 25, 2022)
16-4693872-C-T		not specified	Uncertain significance (Apr 07, 2022)
16-4693987-C-T		not specified	Uncertain significance (Jun 22, 2023)
16-4694090-T-C		not specified	Uncertain significance (Jan 03, 2025)
16-4694103-G-C		not specified	Uncertain significance (Dec 12, 2023)
16-4694135-G-A		not specified	Uncertain significance (Jun 09, 2022)
16-4694153-C-T		not specified	Uncertain significance (Mar 06, 2025)
16-4694177-C-T		not specified	Uncertain significance (Feb 09, 2025)
16-4694194-G-A		not specified	Uncertain significance (Feb 03, 2022)
16-4694197-G-A		not specified	Uncertain significance (Oct 03, 2022)
16-4694960-G-A		not specified	Likely benign (Jan 07, 2025)
16-4694963-G-A		not specified	Likely benign (Dec 23, 2024)
16-4694974-G-C		not specified	Uncertain significance (Feb 19, 2025)
16-4694993-G-A		not specified	Likely benign (Dec 01, 2024)
16-4695014-C-A		not specified	Uncertain significance (Feb 13, 2024)
16-4695023-C-T		not specified	Likely benign (Sep 29, 2023)
16-4695029-C-T		not specified	Likely benign (Aug 14, 2023)
16-4695046-C-T		not specified	Uncertain significance (Jan 02, 2024)
16-4695078-G-T		not specified	Uncertain significance (Oct 29, 2021)
16-4695096-G-A		not specified	Uncertain significance (Nov 21, 2022)
16-4695104-G-C		not specified	Uncertain significance (Oct 22, 2024)
16-4695144-A-G		not specified	Uncertain significance (Jul 20, 2021)
16-4695145-A-C		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT16L1	protein_coding	protein_coding	ENST00000304301	3	2166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000125	0.408	125582	0	18	125600	0.0000717

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.763	93	116	0.801	0.00000615	1307
Missense in Polyphen		24	43.508	0.55162		491
Synonymous	-5.91	114	57.1	1.99	0.00000335	448
Loss of Function	0.139	6	6.38	0.940	3.60e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000405	0.000405
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000692	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000194	0.0000176
Middle Eastern	0.0000692	0.0000544
South Asian	0.0000370	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Key regulator of TP53BP1 required to stabilize TP53BP1 and regulate its recruitment to chromatin (PubMed:28241136). In absence of DNA damage, interacts with the tandem Tudor-like domain of TP53BP1, masking the region that binds histone H4 dimethylated at 'Lys-20' (H4K20me2), thereby preventing TP53BP1 recruitment to chromatin and maintaining TP53BP1 localization to the nucleus (PubMed:28241136). Following DNA damage, ATM-induced phosphorylation of TP53BP1 and subsequent recruitment of RIF1 leads to dissociate NUDT16L1/TIRR from TP53BP1, unmasking the tandem Tudor-like domain and allowing recruitment of TP53BP1 to DNA double strand breaks (DSBs) (PubMed:28241136). Binds U8 snoRNA (PubMed:18820299). {ECO:0000269|PubMed:18820299, ECO:0000269|PubMed:28241136}.
• Pathway: Proteoglycans in cancer - Homo sapiens (human);Syndecan-4-mediated signaling events (Consensus)

Intolerance Scores

• loftool: 0.154
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.309
• hipred: N
• hipred_score: 0.282
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.230

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudt16l1

Gene ontology

• Biological process: negative regulation of double-strand break repair via nonhomologous end joining
• Cellular component: nucleus
• Molecular function: RNA binding;protein binding;snoRNA binding;protein homodimerization activity;m7G(5')pppN diphosphatase activity