TYW3

tRNA-yW synthesizing protein 3 homolog

Basic information

Region (hg38): 1:74733151-74766678

Previous symbols: [ "C1orf171" ]

Links

ENSG00000162623 ∙ NCBI:127253 ∙ OMIM:611245 ∙ HGNC:24757 ∙ Uniprot:Q6IPR3 ∙ 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 TYW3 gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TYW3 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 TYW3

This is a list of pathogenic ClinVar variants found in the TYW3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-74733293-A-C		not specified	Uncertain significance (Jul 19, 2023)
1-74736560-G-T		not specified	Uncertain significance (Jan 08, 2024)
1-74738690-A-G		not specified	Uncertain significance (Dec 02, 2021)
1-74738719-T-A		not specified	Uncertain significance (Apr 11, 2023)
1-74738724-C-G		not specified	Uncertain significance (Dec 31, 2023)
1-74752328-A-G		not specified	Uncertain significance (Jan 03, 2022)
1-74752349-G-A		not specified	Uncertain significance (Dec 16, 2023)
1-74752364-A-G		not specified	Uncertain significance (Apr 26, 2023)
1-74763925-A-G		not specified	Uncertain significance (Feb 10, 2022)
1-74763937-A-T		not specified	Uncertain significance (May 18, 2023)
1-74763940-A-G		not specified	Uncertain significance (Dec 20, 2023)
1-74764007-A-G		not specified	Uncertain significance (Mar 28, 2023)
1-74764015-C-T		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TYW3	protein_coding	protein_coding	ENST00000370867	6	33527

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00169	0.901	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.357	149	137	1.09	0.00000646	1733
Missense in Polyphen		40	42.237	0.94704		526
Synonymous	-0.397	51	47.5	1.07	0.00000214	448
Loss of Function	1.44	6	11.2	0.535	5.38e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000125
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000721	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.000144	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable S-adenosyl-L-methionine-dependent methyltransferase 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 (By similarity). {ECO:0000250}.
• Pathway: Synthesis of wybutosine at G37 of tRNA(Phe);tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA;wybutosine biosynthesis;7-(3-amino-3-carboxypropyl)-wyosine biosynthesis (Consensus)

Recessive Scores

• pRec: 0.0776

Intolerance Scores

• loftool: 0.790
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.0435
• hipred: N
• hipred_score: 0.355
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.551

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tyw3

Gene ontology

• Biological process: tRNA methylation;wybutosine biosynthetic process
• Cellular component: cytoplasm
• Molecular function: tRNA methyltransferase activity