UBOX5

protein-coding

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

Gene summary

This gene encodes a U-box domain containing protein. The encoded protein interacts with E2 enzymes and may play a role in the ubiquitination pathway. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

MANE transcript

NM_014948.4

Inheritance

—

ClinVar variants

U:63B:6

Top phenotype

Mitochondrial complex IV deficiency, nuclear type 24

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr20:3,107,573-3,160,196

External References & Databases

Ensembl (ENSG00000185019)

Transcript & Mutation Effects

hg38 • Region Span ~52.6 kb

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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 UBOX5 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 171

Mitochondrial complex IV deficiency, nuclear type 24Total: 5

Leigh syndromeTotal: 5

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014948.4. 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					1 clinvar	1
missense			62 clinvar	5 clinvar		67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	63	5	1	69

Highest pathogenic variant AF is 0.00006752462

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014948.4	RefSeq	NP_055763.1	4	MANE Select
ENST00000217173.7	Ensembl	ENSP00000217173.2	4	MANE Select
NM_001267584.2	RefSeq	NP_001254513.1	4	Standard
NM_199415.3	RefSeq	NP_955447.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ubiquitin mediated proteolysis - Homo sapiens (human)
Immune System
Adaptive Immune System
Antigen processing: Ubiquitination & Proteasome degradation
Class I MHC mediated antigen processing & presentation

Biological Process

protein polyubiquitination

Molecular Function

protein binding
ubiquitin protein ligase binding
ubiquitin-ubiquitin ligase activity
metal ion binding
ubiquitin protein ligase activity

Cellular Component

nucleus
nucleoplasm
focal adhesion
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000217173
Coding exons: 4
Length: 52624
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125748
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.927	259	305	0.851	0.0000166	3507
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.000097	0.000097	rare
South Asian	0.00016	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Intolerance Scores

LoFtool: 0.646
RVIS EVS: -0.4
RVIS percentile EVS: 26.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.848

Gene Damage Prediction

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