UBXN11

UBX domain protein 11, the group of UBX domain containing

Basic information

Region (hg38): 1:26281327-26318363

Previous symbols: [ "UBXD5" ]

Links

ENSG00000158062 ∙ NCBI:91544 ∙ OMIM:609151 ∙ HGNC:30600 ∙ Uniprot:Q5T124 ∙ 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 UBXN11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBXN11 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						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	23	2	0

Variants in UBXN11

This is a list of pathogenic ClinVar variants found in the UBXN11 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-26282320-TCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA-T		Hepatocellular carcinoma • Small cell lung carcinoma • Lung cancer	Pathogenic (Jun 15, 2021)
1-26282328-AGGGACTGGGGCCGGGACCGGGACC-A		Hepatocellular carcinoma • Lung cancer	Pathogenic (Jun 15, 2021)
1-26282328-A-AGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACC		Hepatocellular carcinoma • Lung cancer	Pathogenic (Jun 15, 2021)
1-26282328-A-AGGGACTGGGGCCGGGACCGGGACC		Hepatocellular carcinoma • Lung cancer	Pathogenic (Jun 15, 2021)
1-26282334-TGGGGCCG-T		Hepatocellular carcinoma • Lung cancer	Pathogenic (Jun 15, 2021)
1-26282344-ACCGGGACCGGGACTGGG-A		Hepatocellular carcinoma • Lung cancer	Pathogenic (Jun 15, 2021)
1-26282370-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-26282374-ACC-A		Hepatocellular carcinoma • Lung cancer • Small cell lung carcinoma	Pathogenic (Jun 15, 2021)
1-26282385-G-T		not specified	Uncertain significance (May 30, 2024)
1-26282386-GCCGGGA-G		Hepatocellular carcinoma • Small cell lung carcinoma • Lung cancer	Pathogenic (Jun 15, 2021)
1-26282406-A-C		not specified	Likely benign (Jan 03, 2024)
1-26282447-C-G		not specified	Uncertain significance (Mar 15, 2024)
1-26282453-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-26282504-G-C		not specified	Uncertain significance (Nov 02, 2021)
1-26282568-C-A		not specified	Uncertain significance (Jul 05, 2023)
1-26282686-T-C		not specified	Uncertain significance (Mar 24, 2023)
1-26282738-G-C		not specified	Uncertain significance (Dec 22, 2023)
1-26282743-G-A		not specified	Uncertain significance (Dec 06, 2021)
1-26282874-C-T		not specified	Uncertain significance (Aug 16, 2022)
1-26282891-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-26282916-G-A		not specified	Uncertain significance (Jul 20, 2021)
1-26284210-G-T		not specified	Uncertain significance (Jul 14, 2021)
1-26284398-T-C		not specified	Uncertain significance (Jul 20, 2021)
1-26285516-C-T		not specified	Uncertain significance (Mar 20, 2023)
1-26285531-C-T		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBXN11	protein_coding	protein_coding	ENST00000374222	14	37036

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.40e-13	0.172	124429	2	404	124835	0.00163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.317	299	315	0.950	0.0000192	3333
Missense in Polyphen		78	90.378	0.86304		1022
Synonymous	-1.82	159	132	1.20	0.00000834	1052
Loss of Function	0.959	23	28.5	0.806	0.00000162	296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0145	0.0144
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.00106	0.00106
Finnish	0.000232	0.000232
European (Non-Finnish)	0.000783	0.000759
Middle Eastern	0.00106	0.00106
South Asian	0.00102	0.00101
Other	0.00183	0.00181

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the reorganization of actin cytoskeleton mediated by RND1, RND2 AND RND3. Promotes RHOA activation mediated by GNA12 and GNA13 (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.206

Intolerance Scores

• loftool: 0.994
• rvis_EVS: 1.2
• rvis_percentile_EVS: 93.01

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.298
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.636

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubxn11

Gene ontology

• Biological process: proteasome-mediated ubiquitin-dependent protein catabolic process
• Cellular component: cytoplasm;cytoskeleton
• Molecular function: protein binding;ubiquitin binding