UBXN10

UBX domain protein 10, the group of UBX domain containing

Basic information

Region (hg38): 1:20186096-20196050

Previous symbols: [ "UBXD3" ]

Links

ENSG00000162543

∙ NCBI:127733 ∙ OMIM:616783 ∙ HGNC:26354 ∙ Uniprot:Q96LJ8 ∙ 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 UBXN10 gene.

not_specified (41 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBXN10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152376.5. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			37 clinvar	4 clinvar		41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	37	4	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBXN10	protein_coding	protein_coding	ENST00000375099	1	9964

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0139	0.878	125180	0	568	125748	0.00226

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.235	151	159	0.948	0.00000899	1810
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00348	0.00348
Ashkenazi Jewish	0.000498	0.000496
East Asian	0.00147	0.00147
Finnish	0.000924	0.000924
European (Non-Finnish)	0.00353	0.00354
Middle Eastern	0.00147	0.00147
South Asian	0.000425	0.000392
Other	0.00195	0.00196

dbNSFP

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

Haploinsufficiency Scores

pHI: 0.118
hipred: N
hipred_score: 0.153
ghis: 0.517

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.138

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ubxn10
Phenotype

Zebrafish Information Network

Gene name: ubxn10
Affected structure: heart tube
Phenotype tag: abnormal
Phenotype quality: mislocalised

Gene ontology

Biological process: cilium assembly
Cellular component: cilium;intraciliary transport particle B
Molecular function: protein binding