UBXN2A

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

Basic information

Region (hg38): 2:23927284-24004909

Previous symbols: [ "UBXD4" ]

Links

ENSG00000173960 ∙ NCBI:165324 ∙ ∙ HGNC:27265 ∙ Uniprot:P68543 ∙ 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 UBXN2A gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBXN2A 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in UBXN2A

This is a list of pathogenic ClinVar variants found in the UBXN2A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-23971277-G-A		not specified	Uncertain significance (Jan 10, 2023)
2-23971290-G-T		not specified	Uncertain significance (May 27, 2022)
2-23971325-T-C		not specified	Uncertain significance (Aug 02, 2021)
2-23971328-A-T		not specified	Uncertain significance (Feb 28, 2023)
2-23971397-G-A		not specified	Likely benign (May 09, 2022)
2-23982942-G-A		not specified	Uncertain significance (Jan 26, 2022)
2-23982945-G-A		not specified	Uncertain significance (Jun 29, 2022)
2-23982984-A-G		not specified	Uncertain significance (Jan 09, 2024)
2-23982985-C-T		not specified	Uncertain significance (Feb 27, 2024)
2-23982991-C-T		not specified	Uncertain significance (Aug 08, 2022)
2-23984713-G-A		not specified	Uncertain significance (Oct 12, 2021)
2-23984828-A-G		not specified	Uncertain significance (Nov 08, 2022)
2-23999851-A-G		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBXN2A	protein_coding	protein_coding	ENST00000309033	6	77625

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000139	0.399	125721	0	22	125743	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.585	112	131	0.856	0.00000639	1724
Missense in Polyphen		30	35.089	0.85496		487
Synonymous	0.803	43	50.2	0.856	0.00000297	459
Loss of Function	0.546	10	12.0	0.830	5.08e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000610	0.000608
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000622	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000125	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.726
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.177
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.110

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubxn2a

Gene ontology

• Biological process: autophagosome assembly;Golgi organization;regulation of gene expression;regulation of protein ubiquitination;nuclear envelope reassembly;regulation of protein catabolic process;proteasome-mediated ubiquitin-dependent protein catabolic process;membrane fusion;cellular response to leukemia inhibitory factor
• Cellular component: endoplasmic reticulum;cis-Golgi network;cytosol
• Molecular function: protein binding;acetylcholine receptor binding;ubiquitin binding