NUDT21

nudix hydrolase 21, the group of Nudix hydrolase family|Cleavage factor Im complex subunits

Basic information

Region (hg38): 16:56429132-56452199

Previous symbols: [ "CPSF5" ]

Links

ENSG00000167005 ∙ NCBI:11051 ∙ OMIM:604978 ∙ HGNC:13870 ∙ Uniprot:O43809 ∙ 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 NUDT21 gene.

• not provided (2 variants)
• Inborn genetic diseases (1 variants)

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	2
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	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: gnomAD

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: dbNSFP

• 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

• 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

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