UBOX5

U-box domain containing 5, the group of U-box domain containing|Ring finger proteins

Basic information

Region (hg38): 20:3107573-3160196

Links

ENSG00000185019 ∙ NCBI:22888 ∙ OMIM:619675 ∙ HGNC:17777 ∙ Uniprot:O94941 ∙ 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 UBOX5 gene.

• not_specified (149 variants)
• Leigh_syndrome (5 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBOX5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014948.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			53	5		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	5	1

Highest pathogenic variant AF is 0.00006752462

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBOX5	protein_coding	protein_coding	ENST00000217173	4	52624

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000721	0.983	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.927	259	305	0.851	0.0000166	3507
Missense in Polyphen		48	71.536	0.67099		806
Synonymous	-0.299	135	131	1.03	0.00000786	1142
Loss of Function	2.11	8	17.5	0.456	9.16e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000231	0.000231
European (Non-Finnish)	0.0000969	0.0000967
Middle Eastern	0.000163	0.000163
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a ubiquitin-protein ligase activity acting as an E3 ubiquitin-protein ligase or as a ubiquitin-ubiquitin ligase promoting elongation of ubiquitin chains on substrates. {ECO:0000250|UniProtKB:Q925F4}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Intolerance Scores

• loftool: 0.646
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.85

Haploinsufficiency Scores

• pHI: 0.350
• hipred: N
• hipred_score: 0.187
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.848

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubox5
• Phenotype: immune system phenotype; vision/eye phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: protein polyubiquitination
• Cellular component: nucleus;nucleoplasm;focal adhesion;nuclear body
• Molecular function: protein binding;ubiquitin protein ligase binding;ubiquitin-ubiquitin ligase activity;metal ion binding;ubiquitin protein ligase activity