NUDT4
Basic information
Region (hg38): 12:93377882-93408146
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT4 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 | 2 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 2 | 0 | 0 |
Variants in NUDT4
This is a list of pathogenic ClinVar variants found in the NUDT4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-93394690-G-A | not specified | Uncertain significance (Sep 22, 2023) | ||
| 12-93394699-G-A | not specified | Uncertain significance (Dec 06, 2022) | ||
| 12-93398846-G-T | not specified | Uncertain significance (Mar 25, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NUDT4 | protein_coding | protein_coding | ENST00000337179 | 5 | 25366 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.797 | 0.202 | 124203 | 0 | 2 | 124205 | 0.00000805 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.94 | 37 | 88.4 | 0.418 | 0.00000419 | 1113 |
| Missense in Polyphen | 11 | 31.675 | 0.34728 | 410 | ||
| Synonymous | 1.87 | 19 | 32.5 | 0.584 | 0.00000152 | 321 |
| Loss of Function | 2.58 | 1 | 9.64 | 0.104 | 4.91e-7 | 117 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate), PP-InsP4 and [PP]2-InsP4 (bisdiphosphoinositol tetrakisphosphate), suggesting that it may play a role in signal transduction. Also able to catalyze the hydrolysis of dinucleoside oligophosphate Ap6A, but not Ap5A. The major reaction products are ADP and p4a from Ap6A. Also able to hydrolyze 5-phosphoribose 1-diphosphate. Does not play a role in U8 snoRNA decapping activity. Binds U8 snoRNA. {ECO:0000269|PubMed:10777568}.;
- Pathway
- Metabolism;Synthesis of pyrophosphates in the cytosol;Inositol phosphate metabolism
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.506
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.520
- hipred
- N
- hipred_score
- 0.339
- ghis
- 0.564
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Nudt4
- Phenotype
Gene ontology
- Biological process
- calcium-mediated signaling;cyclic-nucleotide-mediated signaling;intracellular signal transduction;inositol phosphate metabolic process;diphosphoinositol polyphosphate metabolic process;diadenosine pentaphosphate catabolic process;diadenosine hexaphosphate catabolic process;adenosine 5'-(hexahydrogen pentaphosphate) catabolic process
- Cellular component
- nucleus;cytoplasm;cytosol
- Molecular function
- endopolyphosphatase activity;protein binding;diphosphoinositol-polyphosphate diphosphatase activity;snoRNA binding;bis(5'-adenosyl)-hexaphosphatase activity;bis(5'-adenosyl)-pentaphosphatase activity;metal ion binding;m7G(5')pppN diphosphatase activity;inositol diphosphate tetrakisphosphate diphosphatase activity;inositol bisdiphosphate tetrakisphosphate diphosphatase activity;inositol diphosphate pentakisphosphate diphosphatase activity;inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity;inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity;inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity;inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity;inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity;inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity