TBL1Y

transducin beta like 1 Y-linked, the group of WD repeat domain containing

Basic information

Region (hg38): Y:6910686-7101970

Links

ENSG00000092377 ∙ NCBI:90665 ∙ OMIM:400033 ∙ HGNC:18502 ∙ Uniprot:Q9BQ87 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• deafness, Y-linked 2 (Limited), mode of inheritance: YL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, Y-linked 2	YL	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	Audiologic/Otolaryngologic	30341416

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBL1Y gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBL1Y 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				3		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding						0
Total	0	0	0	4	0

Variants in TBL1Y

This is a list of pathogenic ClinVar variants found in the TBL1Y 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-7063898-A-T		Deafness, Y-linked 2	Pathogenic (Apr 16, 2019)
Y-7063916-G-T			Likely benign (Oct 01, 2023)
Y-7064105-G-A		TBL1Y-related disorder	Likely benign (Jan 04, 2023)
Y-7064150-G-C		Deafness, Y-linked 2 • TBL1Y-related disorder	Benign/Likely benign (Aug 10, 2021)
Y-7070228-G-A		TBL1Y-related disorder	Likely benign (Jan 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBL1Y	protein_coding	protein_coding	ENST00000383032	14	180998

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.03e-13	0.00183	67690	127	0	67817	0.000937

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.77	183	85.2	2.15	0.0000138	3474
Missense in Polyphen		85	44.736	1.9		1777
Synonymous	-4.76	72	35.8	2.01	0.00000633	975
Loss of Function	-2.18	15	8.24	1.82	0.00000127	324

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00339	0.00225
Ashkenazi Jewish	0.00	0.00
East Asian	0.0173	0.00865
Finnish	0.000721	0.000355
European (Non-Finnish)	0.000588	0.000283
Middle Eastern	0.0173	0.00865
South Asian	0.000438	0.000219
Other	0.00445	0.00219

dbNSFP

Source: dbNSFP

• Function: FUNCTION: F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of corepressor complexes that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of transcription repressor complexes, thereby allowing cofactor exchange (By similarity). {ECO:0000250}.
• Pathway: Wnt signaling pathway - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• pHI: 0.545
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.119

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;histone deacetylation;negative regulation of nucleic acid-templated transcription
• Cellular component: histone deacetylase complex
• Molecular function: transcription corepressor activity