UTY

protein-coding

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

Gene summary

This gene encodes a protein containing tetratricopeptide repeats which are thought to be involved in protein-protein interactions. The encoded protein is also a minor histocompatibility antigen which may induce graft rejection of male stem cell grafts. A large number of alternatively spliced transcripts have been observed for this gene, but the full length nature of some of these variants has not been determined. [provided by RefSeq, Apr 2012]

MANE transcript

NM_001258249.2

Inheritance

—

ClinVar variants

U:109B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chrY:13,234,577-13,480,673

External References & Databases

Ensembl (ENSG00000183878)

Transcript & Mutation Effects

hg38 • Region Span ~246.1 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to UTY variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001258249.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			16 clinvar			16
missense			70 clinvar	1 clinvar		71
nonsense			7 clinvar			7
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			16 clinvar			16
Total	0	0	109	1	0	110

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 113 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001258249.2	RefSeq	NP_001245178.1	30	MANE Select
ENST00000545955.6	Ensembl	ENSP00000442047.2	30	MANE Select
NM_001258250.1	RefSeq	NP_001245179.1	28	Standard
NM_001258251.1	RefSeq	NP_001245180.1	29	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transcriptional misregulation in cancer - Homo sapiens (human)
HDMs demethylate histones
Chromatin modifying enzymes
Chromatin organization

Biological Process

regulation of gene expression
oxidation-reduction process
histone H3-K27 demethylation

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
chromatin binding
chromatin DNA binding
histone demethylase activity
sequence-specific DNA binding

Cellular Component

nucleus
nucleoplasm
MLL3/4 complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000331397
Coding exons: 28
Length: 232295
Individuals with no LoFs: 67943
Homozygous LoFs: 4
Heterozygous LoFs: 0
Defined: 67947
p: 0.0000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.169	180	174	1.04	0.0000265	8857
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00038	0.00016	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000063	0.000031	rare
South Asian	0.000090	0.000043	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.312

Gene Damage Prediction

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