CTU2

cytosolic thiouridylase subunit 2

Basic information

Region (hg38): 16:88706483-88715396

Previous symbols: [ "C16orf84" ]

Links

ENSG00000174177

∙ NCBI:348180 ∙ OMIM:617057 ∙ HGNC:28005 ∙ Uniprot:Q2VPK5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome (Strong), mode of inheritance: AR
microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome (Limited), mode of inheritance: AR
microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Renal	26633546; 27480277

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CTU2 gene.

not_specified (155 variants)
not_provided (148 variants)
CTU2-related_disorder (40 variants)
Microcephaly,_facial_dysmorphism,_renal_agenesis,_and_ambiguous_genitalia_syndrome (15 variants)
Congenital_anomaly_of_kidney_and_urinary_tract (2 variants)
See_cases (2 variants)
Microcephaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTU2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001012759.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous	1 clinvar		2 clinvar	29 clinvar	10 clinvar	42
missense		2 clinvar	177 clinvar	14 clinvar	9 clinvar	202
nonsense		2 clinvar	2 clinvar			4
start loss						0
frameshift	2 clinvar	1 clinvar		1 clinvar		4
splice donor/acceptor (+/-2bp)		2 clinvar				2
Total	3	7	181	44	19

Highest pathogenic variant AF is 0.0010508368

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTU2	protein_coding	protein_coding	ENST00000453996	15	8924

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.97e-22	0.000324	2997	78910	43805	125712	0.846

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.95	514	316	1.62	0.0000198	3276
Missense in Polyphen		133	82.967	1.603		801
Synonymous	-7.23	243	136	1.79	0.00000917	1051
Loss of Function	-0.533	31	28.0	1.11	0.00000141	311

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	1.74	1.67
Ashkenazi Jewish	0.984	0.892
East Asian	0.919	0.906
Finnish	0.899	0.814
European (Non-Finnish)	0.936	0.843
Middle Eastern	0.919	0.906
South Asian	0.866	0.855
Other	0.926	0.870

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). May act by forming a heterodimer with CTU1/ATPBD3 that ligates sulfur from thiocarboxylated URM1 onto the uridine of tRNAs at wobble position. {ECO:0000255|HAMAP-Rule:MF_03054, ECO:0000269|PubMed:19017811}.;
Pathway: Sulfur relay system - Homo sapiens (human);tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Intolerance Scores

loftool: 0.989
rvis_EVS: 1.43
rvis_percentile_EVS: 95.02

Haploinsufficiency Scores

pHI: 0.280
hipred: N
hipred_score: 0.197
ghis: 0.536

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

Gene name: Ctu2
Phenotype

Gene ontology

Biological process: tRNA wobble uridine modification;tRNA wobble position uridine thiolation;protein urmylation;tRNA thio-modification
Cellular component: cytosol;protein-containing complex
Molecular function: tRNA binding;protein binding;nucleotidyltransferase activity;sulfurtransferase activity