UTY

ubiquitously transcribed tetratricopeptide repeat containing, Y-linked, the group of Lysine demethylases|Tetratricopeptide repeat domain containing|Minor histocompatibility antigens

Basic information

Region (hg38): Y:13234577-13480673

Links

ENSG00000183878

∙ NCBI:7404 ∙ OMIM:400009 ∙ HGNC:12638 ∙ Uniprot:O14607 ∙ 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 UTY gene.

Variants pathogenicity by type

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

Variants in UTY

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

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

Position	Type	Phenotype	Significance	ClinVar
Y-13323634-C-T		not specified	Likely benign (Jun 22, 2023)	2595555

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UTY	protein_coding	protein_coding	ENST00000331397	28	232295

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.967	0.0332	67943	4	0	67947	0.0000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.169	180	174	1.04	0.0000265	8857
Missense in Polyphen		25	55.963	0.44672		2932
Synonymous	-3.91	101	61.8	1.63	0.00000974	2543
Loss of Function	3.66	2	19.4	0.103	0.00000307	908

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000379	0.000162
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000634	0.0000315
Middle Eastern	0.00	0.00
South Asian	0.0000897	0.0000433
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Male-specific histone demethylase that catalyzes trimethylated 'Lys-27' (H3K27me3) demethylation in histone H3. Has relatively low lysine demethylase activity. {ECO:0000269|PubMed:24798337}.;
Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization (Consensus)

Haploinsufficiency Scores

pHI: 0.758
hipred: N
hipred_score: 0.183
ghis: 0.394

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: N
gene_indispensability_score: 0.312

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Uty
Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; muscle phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: regulation of gene expression;oxidation-reduction process;histone H3-K27 demethylation
Cellular component: nucleus;nucleoplasm;MLL3/4 complex
Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;chromatin binding;chromatin DNA binding;histone demethylase activity;sequence-specific DNA binding;metal ion binding;dioxygenase activity;histone demethylase activity (H3-K27 specific)