NUDT11
protein-codingnudix hydrolase 11, the group of Nudix hydrolase family
Gene summary
NUDT11 belongs to a subgroup of phosphohydrolases that preferentially attack diphosphoinositol polyphosphates (Hidaka et al., 2002 [PubMed 12105228]).[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NUDT11 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018159.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 4 | 6 | ||
| missense | 6 | 6 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 9 | 1 | 4 | 14 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060629.2 | 2 | MANE Select | |
| Ensembl | ENSP00000365160.3 | 2 | MANE Select | |
| Ensembl | ENSP00000795646.1 | 2 | Standard | |
| Ensembl | ENSP00000810616.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism
- Synthesis of pyrophosphates in the cytosol
- Inositol phosphate metabolism
Biological Process
- inositol phosphate metabolic process
- diphosphoinositol polyphosphate metabolic process
- diadenosine pentaphosphate catabolic process
- diadenosine hexaphosphate catabolic process
- adenosine 5'-(hexahydrogen pentaphosphate) catabolic process
Molecular Function
- endopolyphosphatase activity
- diphosphoinositol-polyphosphate diphosphatase activity
- bis(5'-adenosyl)-hexaphosphatase activity
- bis(5'-adenosyl)-pentaphosphatase activity
- metal ion binding
Cellular Component
- nucleus
- cytoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000375992
- Coding exons
- 1
- Length
- 6586
- Individuals with no LoFs
- 125670
- Homozygous LoFs
- 3
- Heterozygous LoFs
- 0
- Defined
- 125673
- p
- 0.0000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.46 | 31 | 63.9 | 0.485 | 0.00000422 | 1053 |
| Missense (PolyPhen) | 4 | 25.167 | 0.15894 | 393 | ||
| Synonymous | -2.30 | 46 | 30.0 | 1.53 | 0.00000202 | 330 |
| Loss of Function | 1.23 | 2 | 4.95 | 0.404 | 3.14e-7 | 81 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000067 | 0.000046 | rare |
| European (Non-Finnish) | 0.000012 | 0.0000088 | rare |
| South Asian | 0.000052 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate), suggesting that it may play a role in signal transduction. Also able to catalyze the hydrolysis of dinucleoside oligophosphates, with Ap6A and Ap5A being the preferred substrates. The major reaction products are ADP and p4a from Ap6A and ADP and ATP from Ap5A. Also able to hydrolyze 5-phosphoribose 1-diphosphate. {ECO:0000269|PubMed:12105228}.;
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- LoFtool
- 0.193
- RVIS EVS
- -0.08
- RVIS percentile EVS
- 47.79
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.184
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |