UBXN4

UBX domain protein 4, the group of UBX domain containing

Basic information

Region (hg38): 2:135741734-135785056

Previous symbols: [ "UBXDC1", "UBXD2" ]

Links

ENSG00000144224 ∙ NCBI:23190 ∙ OMIM:611216 ∙ HGNC:14860 ∙ Uniprot:Q92575 ∙ 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 UBXN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBXN4 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in UBXN4

This is a list of pathogenic ClinVar variants found in the UBXN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-135741951-A-G		not specified	Uncertain significance (Apr 13, 2022)
2-135748361-T-A		not specified	Uncertain significance (May 25, 2022)
2-135754243-A-G		not specified	Uncertain significance (Aug 06, 2021)
2-135754265-C-A		not specified	Uncertain significance (Jun 07, 2024)
2-135754273-G-A		not specified	Likely benign (May 26, 2024)
2-135755553-G-A		not specified	Uncertain significance (Dec 21, 2022)
2-135755631-A-G		not specified	Uncertain significance (Aug 08, 2023)
2-135755643-C-T		not specified	Uncertain significance (Jun 09, 2022)
2-135755682-A-G		not specified	Uncertain significance (Apr 19, 2023)
2-135761848-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-135770635-A-G		not specified	Uncertain significance (Aug 10, 2023)
2-135770698-G-A		not specified	Uncertain significance (Aug 08, 2022)
2-135772420-G-A		not specified	Uncertain significance (Dec 14, 2022)
2-135772442-G-A		not specified	Uncertain significance (Jun 02, 2024)
2-135772504-G-A		not specified	Uncertain significance (Apr 23, 2024)
2-135772540-G-C		not specified	Uncertain significance (Aug 30, 2022)
2-135776257-C-G		not specified	Uncertain significance (Jun 09, 2022)
2-135778982-C-T		not specified	Uncertain significance (Aug 02, 2023)
2-135778987-A-G		not specified	Uncertain significance (Jun 24, 2022)
2-135779002-G-A		not specified	Uncertain significance (Dec 06, 2022)
2-135779035-C-G		not specified	Uncertain significance (Mar 30, 2024)
2-135780210-C-T		not specified	Uncertain significance (May 15, 2023)
2-135780294-T-A		not specified	Uncertain significance (May 04, 2023)
2-135780310-C-T		not specified	Uncertain significance (Oct 06, 2021)
2-135780373-A-G		not specified	Uncertain significance (Jan 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBXN4	protein_coding	protein_coding	ENST00000272638	13	43437

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.146	0.854	124771	0	23	124794	0.0000922

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	193	259	0.745	0.0000128	3308
Missense in Polyphen		25	50.506	0.49499		643
Synonymous	-0.0173	91	90.8	1.00	0.00000478	953
Loss of Function	3.64	7	27.7	0.253	0.00000139	361

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000199	0.000199
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000982	0.0000971
Middle Eastern	0.00	0.00
South Asian	0.000143	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in endoplasmic reticulum-associated protein degradation (ERAD). Acts as a platform to recruit both UBQLN1 and VCP to the ER during ERAD (PubMed:19822669). {ECO:0000269|PubMed:16968747, ECO:0000269|PubMed:19822669}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.344
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.612
• hipred: Y
• hipred_score: 0.783
• ghis: 0.650

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.940

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubxn4

Zebrafish Information Network

• Gene name: ubxn4
• Affected structure: melanophore stripe
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: response to unfolded protein;ubiquitin-dependent ERAD pathway
• Cellular component: nuclear envelope;endoplasmic reticulum;endoplasmic reticulum membrane;cytosol
• Molecular function: protein binding