UBXN10

protein-coding

UBX domain protein 10, the group of UBX domain containing

Gene summary

Predicted to enable ubiquitin binding activity. Involved in cilium assembly. Located in cilium and intraciliary transport particle B. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

UBXD3

MANE transcript

NM_152376.5

Inheritance

—

ClinVar variants

U:41B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.49

Max pathogenic AF

—

Genomic locus

chr1:20,186,096-20,196,050

External References & Databases

Ensembl (ENSG00000162543)

Transcript & Mutation Effects

hg38 • Region Span ~10.0 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 UBXN10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 45

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152376.5. 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						0
missense			41 clinvar	4 clinvar		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	4	0	45

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152376.5	RefSeq	NP_689589.1	1	MANE Select
ENST00000375099.4	Ensembl	ENSP00000364240.3	1	MANE Select
ENST00000866634.1	Ensembl	ENSP00000536693.1	1	Standard
ENST00000866634.2	Ensembl	ENSP00000536693.1	1	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ubxn10	Danio rerio	Structure: heart tube Quality: mislocalised abnormal

Gene / Model

Organism

Observed Phenotype

ubxn10

Danio rerio

Structure: heart tube

Quality: mislocalised

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cilium assembly

Molecular Function

protein binding

Cellular Component

cilium
intraciliary transport particle B

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375099
Coding exons: 1
Length: 9964
Individuals with no LoFs: 125180
Homozygous LoFs: 0
Heterozygous LoFs: 568
Defined: 125748
p: 0.00226

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.235	151	159	0.948	0.00000899	1810
Missense (PolyPhen)		37	42.732	0.86586		490
Synonymous	-0.0261	64	63.7	1.00	0.00000382	597
Loss of Function	1.33	4	8.10	0.494	5.18e-7	86

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0017	0.0017	notable
Latino/Admixed American	0.0018	0.0018	notable
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.0015	0.0015	notable
Finnish	0.00092	0.00092	rare
European (Non-Finnish)	0.0035	0.0035	notable
South Asian	0.00043	0.00039	rare
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: VCP/p97-binding protein required for ciliogenesis (PubMed:26389662). Acts as a tethering factor that facilitates recruitment of VCP/p97 to the intraflagellar transport complex B (IFT-B) in cilia (PubMed:26389662). UBX domain-containing proteins act as tethering factors for VCP/p97 and may specify substrate specificity of VCP/p97 (PubMed:26389662). {ECO:0000269|PubMed:26389662}.;

Recessive Scores

pRec: 0.0843

Intolerance Scores

LoFtool: 0.295
RVIS EVS: -0.23
RVIS percentile EVS: 37.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.138

Gene Damage Prediction

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