UBD

ubiquitin D

Basic information

Region (hg38): 6:29555514-29559732

Links

ENSG00000213886 ∙ NCBI:10537 ∙ OMIM:606050 ∙ HGNC:18795 ∙ Uniprot:O15205 ∙ 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 UBD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBD 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			4	2		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	2	0

Variants in UBD

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

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

Position	Type	Phenotype	Significance	ClinVar
6-29555916-G-T		not specified	Uncertain significance (Oct 16, 2023)
6-29555933-C-T			Likely benign (Jun 25, 2018)
6-29556148-G-A		not specified	Uncertain significance (Apr 05, 2023)
6-29556179-C-T		not specified	Uncertain significance (Oct 05, 2023)
6-29556340-C-T		not specified	Likely benign (Feb 28, 2024)
6-29559690-A-T		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBD	protein_coding	protein_coding	ENST00000377050	2	4411

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00705	0.547	123379	1	54	123434	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.236	85	91.3	0.931	0.00000489	1066
Missense in Polyphen		23	23.841	0.96471		331
Synonymous	0.418	33	36.2	0.912	0.00000200	326
Loss of Function	0.0758	3	3.15	0.954	1.31e-7	48

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00134	0.00134
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000903	0.0000902
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000329
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ubiquitin-like protein modifier which can be covalently attached to target protein and subsequently leads to their degradation by the 26S proteasome, in a NUB1-dependent manner. Probably functions as a survival factor. Conjugation ability activated by UBA6. Promotes the expression of the proteasome subunit beta type-9 (PSMB9/LMP2). Regulates TNF-alpha-induced and LPS-mediated activation of the central mediator of innate immunity NF-kappa-B by promoting TNF-alpha-mediated proteasomal degradation of ubiquitinated-I-kappa-B-alpha. Required for TNF-alpha-induced p65 nuclear translocation in renal tubular epithelial cells (RTECs). May be involved in dendritic cell (DC) maturation, the process by which immature dendritic cells differentiate into fully competent antigen-presenting cells that initiate T-cell responses. Mediates mitotic non-disjunction and chromosome instability, in long-term in vitro culture and cancers, by abbreviating mitotic phase and impairing the kinetochore localization of MAD2L1 during the prometaphase stage of the cell cycle. May be involved in the formation of aggresomes when proteasome is saturated or impaired. Mediates apoptosis in a caspase-dependent manner, especially in renal epithelium and tubular cells during renal diseases such as polycystic kidney disease and Human immunodeficiency virus (HIV)- associated nephropathy (HIVAN). {ECO:0000269|PubMed:15831455, ECO:0000269|PubMed:16495226, ECO:0000269|PubMed:16495380, ECO:0000269|PubMed:17889673, ECO:0000269|PubMed:18574467, ECO:0000269|PubMed:19028597, ECO:0000269|PubMed:19033385, ECO:0000269|PubMed:19166848, ECO:0000269|PubMed:19726511, ECO:0000269|PubMed:19959714}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Intolerance Scores

• loftool: 0.501
• rvis_EVS: 1.66
• rvis_percentile_EVS: 96.23

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.581
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.543

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubd
• Phenotype: cellular phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: proteolysis;ubiquitin-dependent protein catabolic process;protein ubiquitination;protein modification by small protein conjugation;response to interferon-gamma;response to tumor necrosis factor;myeloid dendritic cell differentiation;positive regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;post-translational protein modification;aggresome assembly;regulation of mitotic cell cycle phase transition
• Cellular component: fibrillar center;nucleus;cytoplasm;cytosol;aggresome
• Molecular function: protein binding;proteasome binding