UBXN11

protein-coding

UBX domain protein 11, the group of UBX domain containing

Gene summary

This gene encodes a protein with a divergent C-terminal UBX domain. The homologous protein in the rat interacts with members of the Rnd subfamily of Rho GTPases at the cell periphery through its C-terminal region. It also interacts with several heterotrimeric G proteins through their G-alpha subunits and promotes Rho GTPase activation. It is proposed to serve a bidirectional role in the promotion and inhibition of Rho activity through upstream signaling pathways. The 3' coding sequence of this gene contains a polymoprhic region of 24 nt tandem repeats. Several transcripts containing between 1.5 and five repeat units have been reported. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Previous symbols:

UBXD5

MANE transcript

NM_001389556.1

Inheritance

—

ClinVar variants

U:99B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr1:26,281,328-26,318,363

External References & Databases

Ensembl (ENSG00000158062)

Transcript & Mutation Effects

hg38 • Region Span ~37.0 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to UBXN11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 87

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001389556.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar			4
missense			84 clinvar	8 clinvar		92
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	99	8	0	107

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001389556.1	RefSeq	NP_001376485.1	14	MANE Select
ENST00000374222.6	Ensembl	ENSP00000363339.1	14	MANE Select
NM_001077262.2	RefSeq	NP_001070730.1	10	Standard
NM_001389559.1	RefSeq	NP_001376488.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

proteasome-mediated ubiquitin-dependent protein catabolic process

Molecular Function

protein binding
ubiquitin binding

Cellular Component

cytoplasm
cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374222
Coding exons: 14
Length: 37036
Individuals with no LoFs: 124429
Homozygous LoFs: 2
Heterozygous LoFs: 404
Defined: 124835
p: 0.00163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.317	299	315	0.950	0.0000192	3333
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.013	0.013	notable
Latino/Admixed American	0.0015	0.0015	notable
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0011	0.0011	notable
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00078	0.00076	rare
South Asian	0.0010	0.0010	notable
Other	0.0018	0.0018	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.636

Gene Damage Prediction

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