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.

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.

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			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	1

Variants in UBXN10

This is a list of pathogenic ClinVar variants found in the UBXN10 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-20190662-T-C		not specified	Uncertain significance (Feb 24, 2023)
1-20190663-G-GCACATGATAAGGCCCAAGTCC			Benign (May 08, 2020)
1-20190691-G-A		not specified	Uncertain significance (Jun 07, 2024)
1-20190704-C-T		not specified	Uncertain significance (Nov 11, 2024)
1-20190712-C-G		not specified	Uncertain significance (Dec 15, 2023)
1-20190725-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-20190739-G-A		not specified	Uncertain significance (May 16, 2023)
1-20190821-C-A		not specified	Uncertain significance (Apr 20, 2023)
1-20190823-C-T		not specified	Uncertain significance (Jan 31, 2022)
1-20190986-T-C		not specified	Uncertain significance (Nov 06, 2023)
1-20190998-G-A		not specified	Likely benign (Jul 20, 2022)
1-20191015-G-A		not specified	Uncertain significance (Jun 11, 2021)
1-20191037-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-20191061-C-T		not specified	Uncertain significance (Nov 11, 2024)
1-20191069-G-A		not specified	Likely benign (Oct 29, 2021)
1-20191103-A-T		not specified	Uncertain significance (Sep 30, 2024)
1-20191208-G-A		not specified	Uncertain significance (Jan 09, 2023)
1-20191249-C-G		not specified	Uncertain significance (Dec 12, 2023)
1-20191303-A-T		not specified	Uncertain significance (Dec 05, 2022)
1-20191304-G-A		not specified	Uncertain significance (May 28, 2024)
1-20191307-G-A		not specified	Uncertain significance (Dec 13, 2022)
1-20191312-T-A		not specified	Uncertain significance (Jun 21, 2023)
1-20191325-C-T		not specified	Uncertain significance (Jun 21, 2023)
1-20191343-G-T		not specified	Uncertain significance (Sep 01, 2021)
1-20191374-C-G		not specified	Uncertain significance (Jan 11, 2023)

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

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