TYW5

tRNA-yW synthesizing protein 5, the group of JmjC hydroxylases

Basic information

Region (hg38): 2:199928912-199955736

Previous symbols: [ "C2orf60" ]

Links

ENSG00000162971 ∙ NCBI:129450 ∙ OMIM:619882 ∙ HGNC:26754 ∙ Uniprot:A2RUC4 ∙ 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 TYW5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TYW5 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						0
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in TYW5

This is a list of pathogenic ClinVar variants found in the TYW5 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-199933071-T-A		not specified	Uncertain significance (Mar 18, 2024)
2-199933094-G-C		not specified	Uncertain significance (Mar 18, 2024)
2-199933116-C-T		not specified	Uncertain significance (Jun 01, 2023)
2-199933119-C-T		not specified	Uncertain significance (Feb 22, 2023)
2-199933165-T-G		not specified	Uncertain significance (Jan 02, 2024)
2-199936458-T-C		not specified	Uncertain significance (Nov 18, 2023)
2-199948429-G-T		not specified	Uncertain significance (Sep 29, 2023)
2-199948432-C-T		not specified	Uncertain significance (Nov 01, 2022)
2-199948462-A-T		not specified	Uncertain significance (Sep 27, 2021)
2-199948471-C-G		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TYW5	protein_coding	protein_coding	ENST00000354611	8	25762

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.95e-10	0.233	124718	0	76	124794	0.000305

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.120	158	162	0.974	0.00000760	2061
Missense in Polyphen		52	50.982	1.02		636
Synonymous	1.19	46	57.4	0.801	0.00000256	572
Loss of Function	0.740	17	20.6	0.824	0.00000120	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000447	0.000446
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000167
Finnish	0.000749	0.000742
European (Non-Finnish)	0.000294	0.000291
Middle Eastern	0.000167	0.000167
South Asian	0.000430	0.000425
Other	0.000501	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: tRNA hydroxylase that acts as a component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes the hydroxylation of 7-(a-amino-a-carboxypropyl)wyosine (yW-72) into undermodified hydroxywybutosine (OHyW*). OHyW* being further transformed into hydroxywybutosine (OHyW) by LCMT2/TYW4. OHyW is a derivative of wybutosine found in higher eukaryotes. {ECO:0000269|PubMed:20739293}.
• Pathway: Synthesis of wybutosine at G37 of tRNA(Phe);tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.204
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tyw5

Gene ontology

• Biological process: tRNA modification;wybutosine biosynthetic process;oxidation-reduction process
• Cellular component: cytoplasm
• Molecular function: tRNA binding;iron ion binding;2-oxoglutarate-dependent dioxygenase activity;protein homodimerization activity;tRNAPhe (7-(3-amino-3-carboxypropyl)wyosine37-C2)-hydroxylase activity