UBXN2B

UBX domain protein 2B, the group of UBX domain containing

Basic information

Region (hg38): 8:58411359-58451501

Links

ENSG00000215114 ∙ NCBI:137886 ∙ OMIM:610686 ∙ HGNC:27035 ∙ Uniprot:Q14CS0 ∙ 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 UBXN2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBXN2B 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in UBXN2B

This is a list of pathogenic ClinVar variants found in the UBXN2B region.

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

Position	Type	Phenotype	Significance	ClinVar
8-58411402-G-C		not specified	Uncertain significance (Aug 08, 2023)
8-58411402-G-T		not specified	Uncertain significance (Jun 02, 2023)
8-58411407-G-C		not specified	Uncertain significance (Jul 27, 2024)
8-58411409-G-T		not specified	Likely benign (Jul 13, 2021)
8-58411426-G-C		not specified	Uncertain significance (May 30, 2024)
8-58411459-G-A		not specified	Uncertain significance (Jun 25, 2024)
8-58416876-T-A		not specified	Uncertain significance (Dec 17, 2023)
8-58416937-C-T		not specified	Uncertain significance (Dec 26, 2023)
8-58416949-C-G		not specified	Uncertain significance (Jan 26, 2022)
8-58416952-C-T		not specified	Uncertain significance (Aug 30, 2021)
8-58433161-C-T		not specified	Uncertain significance (Sep 14, 2022)
8-58434406-G-T		not specified	Uncertain significance (May 03, 2023)
8-58434459-A-G		not specified	Uncertain significance (Apr 01, 2024)
8-58439745-A-G		not specified	Uncertain significance (Jan 24, 2023)
8-58445959-T-A		not specified	Uncertain significance (Jan 27, 2022)
8-58445962-A-G		not specified	Uncertain significance (Apr 24, 2023)
8-58445966-T-C		not specified	Uncertain significance (Oct 25, 2022)
8-58446036-T-A		not specified	Uncertain significance (May 16, 2023)
8-58447407-C-G		not specified	Uncertain significance (Aug 15, 2024)
8-58447456-G-T		not specified	Uncertain significance (Sep 15, 2021)
8-58447486-G-C		not specified	Uncertain significance (Dec 10, 2024)
8-58447517-T-C		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBXN2B	protein_coding	protein_coding	ENST00000399598	8	40238

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.103	0.891	124765	0	13	124778	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.268	148	157	0.940	0.00000811	2141
Missense in Polyphen		53	60.537	0.8755		787
Synonymous	0.703	49	55.7	0.880	0.00000255	646
Loss of Function	2.38	4	13.4	0.298	5.61e-7	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000648	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000232	0.000232
European (Non-Finnish)	0.0000538	0.0000530
Middle Eastern	0.00	0.00
South Asian	0.0000445	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein required for Golgi and endoplasmic reticulum biogenesis (PubMed:17141156). Involved in Golgi and endoplasmic reticulum maintenance during interphase and in their reassembly at the end of mitosis (PubMed:17141156). The complex formed with VCP has membrane fusion activity; membrane fusion activity requires USO1-GOLGA2 tethering and BET1L (PubMed:17141156). VCPIP1 is also required, but not its deubiquitinating activity (PubMed:17141156). Together with NSFL1C/p47, regulates the centrosomal levels of kinase AURKA/Aurora A during mitotic progression by promoting AURKA removal from centrosomes in prophase (PubMed:23649807). Also, regulates spindle orientation during mitosis (PubMed:23649807). {ECO:0000269|PubMed:17141156, ECO:0000269|PubMed:23649807}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.507
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.533
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.677

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubxn2b

Gene ontology

• Biological process: autophagosome assembly;establishment of mitotic spindle orientation;Golgi organization;nuclear envelope reassembly;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of mitotic centrosome separation;membrane fusion;negative regulation of protein localization to centrosome
• Cellular component: nucleus;endoplasmic reticulum;Golgi apparatus;cytosol;spindle pole centrosome
• Molecular function: protein binding;ubiquitin binding