UPK3B

protein-coding

uroplakin 3B

Gene summary

UPK3B is a minor component of the apical plaques of mammalian urothelium that binds and dimerizes with uroplakin-1b (UPK1B; MIM 602380), one of the major conserved urothelium membrane proteins. The other major conserved integral membrane proteins of urothelial plaques are UPK1A (MIM 611557), UPK2 (MIM 611558), and UPK3A (MIM 611559) (Deng et al., 2002 [PubMed 12446744]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_001347684.2

Inheritance

—

ClinVar variants

U:50B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr7:76,510,525-76,516,522

External References & Databases

Ensembl (ENSG00000243566)

NCBI Gene (105375355)

Transcript & Mutation Effects

hg38 • Region Span ~6.0 kb

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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 UPK3B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 84

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001347684.2. 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			9 clinvar	3 clinvar		12
missense			41 clinvar	11 clinvar		52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	14	0	64

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001347684.2	RefSeq	NP_001334613.1	6	MANE Select
ENST00000334348.8	Ensembl	ENSP00000334938.3	6	MANE Select
ENST00000257632.9	Ensembl	ENSP00000257632.5	4	Standard
ENST00000394849.1	Ensembl	ENSP00000378319.1	5	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
upk3b	Danio rerio	Structure: head Quality: morphology abnormal

Gene / Model

Organism

Observed Phenotype

upk3b

Danio rerio

Structure: head

Quality: morphology

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of gene expression

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000419923
Coding exons: 4
Length: 508596
Individuals with no LoFs: 123747
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 123785
p: 0.000153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.193	177	184	0.960	0.0000117	1954
Missense (PolyPhen)		47	49.016	0.95887		548
Synonymous	0.678	72	79.7	0.903	0.00000521	693
Loss of Function	1.06	7	10.8	0.650	6.09e-7	104

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0010	0.00093	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0	0.0	absent
Other	0.00053	0.00050	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the asymmetric unit membrane (AUM); a highly specialized biomembrane elaborated by terminally differentiated urothelial cells. May play an important role in AUM-cytoskeleton interaction in terminally differentiated urothelial cells. It also contributes to the formation of urothelial glycocalyx which may play an important role in preventing bacterial adherence (By similarity). {ECO:0000250}.;

Intolerance Scores

RVIS EVS: 1.11
RVIS percentile EVS: 92.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.00904

Gene Damage Prediction

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