NUDT21
nudix hydrolase 21, the group of Nudix hydrolase family|Cleavage factor Im complex subunits
Basic information
Region (hg38): 16:56429133-56452199
Previous symbols: [ "CPSF5" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 NUDT21 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 | 2 | |||||
| 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 | 2 |
Variants in NUDT21
This is a list of pathogenic ClinVar variants found in the NUDT21 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-56434354-A-G | Benign (May 31, 2018) | |||
| 16-56434401-A-G | Benign (Feb 26, 2018) | |||
| 16-56439685-C-G | not specified | Uncertain significance (Oct 25, 2022) | ||
| 16-56451160-G-A | not specified | Uncertain significance (Feb 06, 2024) | ||
| 16-56451649-C-T | not specified | Uncertain significance (Oct 12, 2021) | ||
| 16-56451650-G-C | not specified | Uncertain significance (Dec 13, 2022) | ||
| 16-56451725-A-G | not specified | Uncertain significance (May 16, 2022) | ||
| 16-56451734-A-T | not specified | Uncertain significance (Sep 17, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NUDT21 | protein_coding | protein_coding | ENST00000300291 | 7 | 23067 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.986 | 0.0142 | 125743 | 0 | 2 | 125745 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.47 | 15 | 124 | 0.121 | 0.00000607 | 1477 |
| Missense in Polyphen | 2 | 41.76 | 0.047893 | 585 | ||
| Synonymous | -1.36 | 56 | 44.5 | 1.26 | 0.00000213 | 435 |
| Loss of Function | 3.33 | 0 | 12.9 | 0.00 | 5.44e-7 | 159 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000882 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs (PubMed:9659921, PubMed:8626397, PubMed:14690600, PubMed:15937220, PubMed:17024186, PubMed:17098938, PubMed:29276085). CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'-end, so called cleavage and polyadenylation signals (pA signals) (PubMed:9659921, PubMed:8626397, PubMed:14690600, PubMed:17024186). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation (PubMed:17098938, PubMed:23187700, PubMed:29276085). The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'- untranslated region (UTR) for a huge number of pre-mRNAs (PubMed:17098938, PubMed:20695905, PubMed:29276085). NUDT21/CPSF5 activates indirectly the mRNA 3'-processing machinery by recruiting CPSF6 and/or CPSF7 (PubMed:29276085). Binds to 5'-UGUA- 3' elements localized upstream of pA signals that act as enhancers of pre-mRNA 3'-end processing (PubMed:8626397, PubMed:14690600, PubMed:15169763, PubMed:17024186, PubMed:22813749, PubMed:20479262). The homodimer mediates simultaneous sequence- specific recognition of two 5'-UGUA-3' elements within the pre- mRNA (PubMed:20479262, PubMed:21295486). Plays a role in somatic cell fate transitions and pluripotency by regulating widespread changes in gene expression through an APA-dependent function (By similarity). Binds to chromatin (By similarity). Binds to, but does not hydrolyze mono- and di-adenosine nucleotides (PubMed:18445629). {ECO:0000250|UniProtKB:Q9CQF3, ECO:0000269|PubMed:14690600, ECO:0000269|PubMed:15169763, ECO:0000269|PubMed:15937220, ECO:0000269|PubMed:17024186, ECO:0000269|PubMed:17098938, ECO:0000269|PubMed:18445629, ECO:0000269|PubMed:20479262, ECO:0000269|PubMed:20695905, ECO:0000269|PubMed:21295486, ECO:0000269|PubMed:22813749, ECO:0000269|PubMed:23187700, ECO:0000269|PubMed:29276085, ECO:0000269|PubMed:8626397, ECO:0000269|PubMed:9659921}.;
- Pathway
- mRNA surveillance pathway - Homo sapiens (human);mRNA Processing;Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Processing of Intronless Pre-mRNAs;Processing of Capped Intronless Pre-mRNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;mRNA Splicing - Major Pathway;mRNA Splicing;mRNA 3,-end processing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.769
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.672
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.964
Mouse Genome Informatics
- Gene name
- Nudt21
- Phenotype
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;termination of RNA polymerase II transcription;mRNA polyadenylation;mRNA processing;posttranscriptional regulation of gene expression;cell differentiation;mRNA 3'-end processing;positive regulation of mRNA cleavage;protein tetramerization;protein heterotetramerization;pre-mRNA cleavage required for polyadenylation;mRNA alternative polyadenylation;positive regulation of mRNA polyadenylation;messenger ribonucleoprotein complex assembly;positive regulation of stem cell differentiation;positive regulation of pro-B cell differentiation
- Cellular component
- nucleus;nucleoplasm;cytoplasm;centrosome;microtubule organizing center;mRNA cleavage and polyadenylation specificity factor complex;mRNA cleavage factor complex;nuclear body;paraspeckles
- Molecular function
- chromatin binding;RNA binding;mRNA binding;protein binding;hydrolase activity;AU-rich element binding;identical protein binding;protein homodimerization activity;histone deacetylase binding