TUT1

terminal uridylyl transferase 1, U6 snRNA-specific, the group of RNA binding motif containing|Terminal nucleotidyltransferases|Non-canonical poly(A) polymerases

Basic information

Region (hg38): 11:62575045-62591637

Previous symbols: [ "RBM21" ]

Links

ENSG00000149016 ∙ NCBI:64852 ∙ OMIM:610641 ∙ HGNC:26184 ∙ Uniprot:Q9H6E5 ∙ 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 TUT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUT1 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				3	2	5
missense		1	55	3	2	61
nonsense						0
start loss						0
frameshift			1		1	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding						0
Total	0	1	56	6	5

Variants in TUT1

This is a list of pathogenic ClinVar variants found in the TUT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62575111-T-C		not specified	Uncertain significance (Dec 17, 2023)
11-62575159-G-A			Benign (Oct 24, 2018)
11-62575194-A-T		not specified	Uncertain significance (Apr 26, 2024)
11-62575197-C-T		not specified	Likely benign (Jul 12, 2023)
11-62575205-C-A			Likely benign (Jan 01, 2023)
11-62575209-G-C		not specified	Uncertain significance (Dec 08, 2023)
11-62575218-G-A		not specified	Uncertain significance (Sep 14, 2023)
11-62575306-C-G		not specified	Uncertain significance (Sep 13, 2023)
11-62575314-C-A		not specified	Uncertain significance (May 31, 2023)
11-62575346-C-T			Benign (Jul 15, 2018)
11-62575356-TG-T			Uncertain significance (Aug 25, 2017)
11-62575380-C-T		not specified	Uncertain significance (Jan 31, 2024)
11-62575434-G-T		not specified	Uncertain significance (Apr 13, 2023)
11-62575481-G-A			Likely benign (Mar 02, 2018)
11-62575506-C-T		not specified	Likely benign (Apr 29, 2024)
11-62575551-G-C		not specified	Uncertain significance (Jun 22, 2024)
11-62575579-G-C		not specified	Uncertain significance (Aug 12, 2021)
11-62575658-G-C			Benign (Oct 24, 2018)
11-62575725-C-G		not specified	Uncertain significance (Feb 28, 2023)
11-62575791-C-T		not specified	Uncertain significance (Aug 30, 2021)
11-62575815-A-T		not specified	Uncertain significance (Feb 14, 2023)
11-62575854-G-A		not specified	Uncertain significance (Jan 04, 2022)
11-62575896-G-A		not specified	Uncertain significance (Apr 18, 2023)
11-62575896-G-C		not specified	Uncertain significance (Sep 27, 2021)
11-62575955-G-T		not specified	Uncertain significance (Mar 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TUT1	protein_coding	protein_coding	ENST00000308436	9	17133

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.55e-11	0.986	125674	0	74	125748	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.422	504	531	0.948	0.0000313	5774
Missense in Polyphen		164	191.26	0.85746		2011
Synonymous	-0.613	230	218	1.05	0.0000121	2026
Loss of Function	2.41	23	39.3	0.585	0.00000236	382

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00141	0.00110
Ashkenazi Jewish	0.000206	0.000198
East Asian	0.000220	0.000217
Finnish	0.000146	0.000139
European (Non-Finnish)	0.000257	0.000255
Middle Eastern	0.000220	0.000217
South Asian	0.000327	0.000327
Other	0.000495	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Poly(A) polymerase that creates the 3'-poly(A) tail of specific pre-mRNAs. Localizes to nuclear speckles together with PIP5K1A and mediates polyadenylation of a select set of mRNAs, such as HMOX1. In addition to polyadenylation, it is also required for the 3'-end cleavage of pre-mRNAs: binds to the 3'UTR of targeted pre-mRNAs and promotes the recruitment and assembly of the CPSF complex on the 3'UTR of pre-mRNAs. In addition to adenylyltransferase activity, also has uridylyltransferase activity. However, the ATP ratio is higher than UTP in cells, suggesting that it functions primarily as a poly(A) polymerase. Acts as a specific terminal uridylyltransferase for U6 snRNA in vitro: responsible for a controlled elongation reaction that results in the restoration of the four 3'-terminal UMP-residues found in newly transcribed U6 snRNA. Not involved in replication- dependent histone mRNA degradation. {ECO:0000269|PubMed:16790842, ECO:0000269|PubMed:18288197, ECO:0000269|PubMed:21102410}.
• Pathway: Pyrimidine metabolism (Consensus)

Recessive Scores

• pRec: 0.0704

Intolerance Scores

• loftool: 0.847
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.45

Haploinsufficiency Scores

• pHI: 0.322
• hipred: Y
• hipred_score: 0.561
• ghis: 0.610

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tut1

Gene ontology

• Biological process: mRNA polyadenylation;snRNA processing;histone mRNA catabolic process;pre-mRNA cleavage required for polyadenylation
• Cellular component: nucleus;nucleolus;cytosol;mRNA cleavage and polyadenylation specificity factor complex;nuclear speck
• Molecular function: RNA binding;mRNA 3'-UTR binding;polynucleotide adenylyltransferase activity;protein binding;ATP binding;enzyme binding;metal ion binding;RNA uridylyltransferase activity