NUDT22

nudix hydrolase 22, the group of Nudix hydrolase family

Basic information

Region (hg38): 11:64225940-64230686

Links

ENSG00000149761 ∙ NCBI:84304 ∙ ∙ HGNC:28189 ∙ Uniprot:Q9BRQ3 ∙ 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 NUDT22 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT22 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	2	0

Variants in NUDT22

This is a list of pathogenic ClinVar variants found in the NUDT22 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64226692-G-A		not specified	Uncertain significance (Feb 17, 2024)
11-64226693-G-A		not specified	Uncertain significance (Apr 27, 2024)
11-64226759-G-A		not specified	Uncertain significance (Aug 31, 2022)
11-64226827-C-T		not specified	Uncertain significance (Jan 22, 2024)
11-64226855-T-A		not specified	Uncertain significance (Sep 27, 2021)
11-64226891-T-C		not specified	Uncertain significance (Jul 25, 2023)
11-64226915-G-A		not specified	Uncertain significance (Jan 07, 2022)
11-64226941-A-G		not specified	Uncertain significance (Jul 26, 2021)
11-64226977-G-A		not specified	Likely benign (May 03, 2023)
11-64226983-G-A		not specified	Uncertain significance (May 24, 2023)
11-64227035-C-A		not specified	Uncertain significance (Apr 19, 2024)
11-64227106-G-A		not specified	Uncertain significance (Feb 06, 2024)
11-64227109-C-A		not specified	Uncertain significance (Mar 18, 2024)
11-64227109-C-T		not specified	Uncertain significance (Jan 06, 2023)
11-64227110-C-G		not specified	Uncertain significance (May 16, 2024)
11-64227607-G-A		not specified	Uncertain significance (May 12, 2024)
11-64227616-C-G		not specified	Uncertain significance (Mar 16, 2022)
11-64227655-A-T		not specified	Uncertain significance (Apr 06, 2024)
11-64229288-G-C		not specified	Uncertain significance (Apr 14, 2022)
11-64229299-G-A		not specified	Uncertain significance (May 01, 2024)
11-64229320-G-A		not specified	Uncertain significance (Jul 06, 2021)
11-64229320-G-C		not specified	Uncertain significance (Oct 26, 2022)
11-64229328-G-A		not specified	Uncertain significance (Nov 07, 2023)
11-64229336-C-G		not specified	Uncertain significance (Apr 23, 2024)
11-64229505-G-C		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT22	protein_coding	protein_coding	ENST00000279206	5	4746

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.52e-7	0.397	125671	0	60	125731	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.998	142	180	0.791	0.00000985	1881
Missense in Polyphen		42	60.213	0.69753		637
Synonymous	1.32	68	83.3	0.816	0.00000486	679
Loss of Function	0.622	11	13.5	0.817	7.54e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000161	0.000152
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000331	0.000326
Finnish	0.0000515	0.0000462
European (Non-Finnish)	0.000433	0.000396
Middle Eastern	0.000331	0.000326
South Asian	0.0000687	0.0000653
Other	0.000174	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes UDP-glucose to glucose 1-phosphate and UMP and UDP-galactose to galactose 1-phosphate and UMP. Preferred substrate is UDP-glucose. {ECO:0000269|PubMed:29413322}.

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.178
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0889

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudt22

Gene ontology

• Cellular component: nucleoplasm
• Molecular function: protein binding;UDP-sugar diphosphatase activity;metal ion binding;GDP-mannose hydrolase activity