CTU1

cytosolic thiouridylase subunit 1

Basic information

Region (hg38): 19:51097606-51108409

Previous symbols: [ "ATPBD3" ]

Links

ENSG00000142544 ∙ NCBI:90353 ∙ OMIM:612694 ∙ HGNC:29590 ∙ Uniprot:Q7Z7A3 ∙ 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 CTU1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTU1 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				1		1
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	0

Variants in CTU1

This is a list of pathogenic ClinVar variants found in the CTU1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51098612-G-A		not specified	Uncertain significance (May 13, 2022)
19-51098627-C-T		not specified	Likely benign (Jun 04, 2024)
19-51098633-G-A		not specified	Uncertain significance (May 09, 2023)
19-51098684-G-C		not specified	Uncertain significance (Sep 22, 2022)
19-51098707-C-T		not specified	Uncertain significance (Sep 12, 2023)
19-51098741-C-A		not specified	Uncertain significance (May 04, 2023)
19-51098741-C-T		not specified	Uncertain significance (Mar 01, 2024)
19-51098761-C-T		not specified	Uncertain significance (Dec 07, 2021)
19-51098762-G-T		not specified	Uncertain significance (Jun 06, 2023)
19-51098798-G-A		not specified	Uncertain significance (Apr 09, 2024)
19-51098800-C-G		not specified	Likely benign (Jan 03, 2024)
19-51098803-G-C		not specified	Uncertain significance (May 08, 2023)
19-51098812-G-T		not specified	Uncertain significance (Oct 25, 2022)
19-51098816-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-51098930-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-51098948-A-G		not specified	Uncertain significance (Apr 20, 2024)
19-51099017-G-C		not specified	Uncertain significance (Dec 12, 2023)
19-51099034-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-51099038-C-A		not specified	Uncertain significance (Jan 08, 2024)
19-51099044-C-T		not specified	Uncertain significance (May 31, 2023)
19-51099058-C-T		not specified	Uncertain significance (Sep 22, 2023)
19-51099092-G-A		not specified	Uncertain significance (Oct 06, 2023)
19-51099122-T-C		not specified	Uncertain significance (Apr 08, 2024)
19-51099139-C-T		not specified	Uncertain significance (Oct 03, 2023)
19-51104109-G-C		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTU1	protein_coding	protein_coding	ENST00000421832	2	10765

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0672	0.747	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	80	136	0.589	0.0000122	2050
Missense in Polyphen		41	55.744	0.73551		781
Synonymous	0.861	60	69.1	0.868	0.00000665	809
Loss of Function	0.901	2	3.93	0.509	1.69e-7	62

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). Directly binds tRNAs and probably acts by catalyzing adenylation of tRNAs, an intermediate required for 2-thiolation. It is unclear whether it acts as a sulfurtransferase that transfers sulfur from thiocarboxylated URM1 onto the uridine of tRNAs at wobble position. {ECO:0000255|HAMAP-Rule:MF_03053, ECO:0000269|PubMed:19017811}.
• Pathway: Sulfur relay system - Homo sapiens (human);tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.120

Haploinsufficiency Scores

• pHI: 0.309
• hipred: N
• hipred_score: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctu1

Gene ontology

• Biological process: tRNA wobble uridine modification;tRNA wobble position uridine thiolation;protein urmylation;tRNA thio-modification
• Cellular component: cytosolic tRNA wobble base thiouridylase complex;cytosol
• Molecular function: tRNA binding;protein binding;nucleotidyltransferase activity