UBTD1

ubiquitin domain containing 1

Basic information

Region (hg38): 10:97498924-97571206

Links

ENSG00000165886 ∙ NCBI:80019 ∙ OMIM:616388 ∙ HGNC:25683 ∙ Uniprot:Q9HAC8 ∙ 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 UBTD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBTD1 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in UBTD1

This is a list of pathogenic ClinVar variants found in the UBTD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-97499207-G-T		not specified	Uncertain significance (Jul 12, 2023)
10-97499250-C-G		not specified	Uncertain significance (Mar 30, 2024)
10-97499257-C-A		not specified	Uncertain significance (Jun 03, 2022)
10-97567916-C-T		not specified	Uncertain significance (Apr 22, 2024)
10-97567917-G-A		not specified	Uncertain significance (Aug 30, 2021)
10-97567976-G-C		not specified	Uncertain significance (Sep 01, 2021)
10-97567994-C-G		not specified	Uncertain significance (Jan 24, 2023)
10-97568013-C-T		not specified	Uncertain significance (Oct 01, 2024)
10-97568066-G-A		not specified	Uncertain significance (Feb 21, 2024)
10-97568093-G-A		not specified	Uncertain significance (Feb 23, 2023)
10-97570143-C-T		not specified	Uncertain significance (Jan 23, 2024)
10-97570171-A-G		not specified	Uncertain significance (Jan 03, 2024)
10-97570174-G-A		not specified	Uncertain significance (Nov 21, 2024)
10-97570198-T-G		not specified	Uncertain significance (Dec 06, 2024)
10-97570224-G-C		not specified	Uncertain significance (Sep 05, 2024)
10-97570231-C-T		not specified	Uncertain significance (Nov 14, 2024)
10-97570272-G-A		not specified	Uncertain significance (Nov 08, 2022)
10-97570278-C-T		not specified	Uncertain significance (Aug 28, 2024)
10-97570279-G-A		not specified	Uncertain significance (Jun 07, 2022)
10-97570288-C-T		not specified	Uncertain significance (Oct 01, 2024)
10-97570299-C-T		not specified	Uncertain significance (Jul 19, 2023)
10-97570389-A-C		not specified	Uncertain significance (Sep 16, 2021)
10-97570392-G-A		not specified	Uncertain significance (Jul 09, 2021)
10-97570422-G-A		not specified	Uncertain significance (Mar 19, 2024)
10-97570440-C-T		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBTD1	protein_coding	protein_coding	ENST00000370664	3	72342

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.746	0.252	125349	0	3	125352	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.482	135	152	0.890	0.0000106	1465
Missense in Polyphen		51	73.735	0.69167		728
Synonymous	0.572	62	68.0	0.912	0.00000497	470
Loss of Function	2.45	1	8.86	0.113	3.80e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000545
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000545	0.0000545
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the regulation of cellular senescence through a positive feedback loop with TP53. Is a TP53 downstream target gene that increases the stability of TP53 protein by promoting the ubiquitination and degradation of MDM2. {ECO:0000269|PubMed:25382750}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.352
• hipred: Y
• hipred_score: 0.507
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.835

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubtd1

Gene ontology

• Molecular function: protein binding