UPK1B

Chr 3

uroplakin 1B

Also known as: TSPAN20, UPIB, UPK1

NCBI Gene: 7348 ENSG00000114638 UniProt: O75841 OMIM: 602380

The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is found in the asymmetrical unit membrane (AUM) where it can form a complex with other transmembrane 4 superfamily proteins. It may play a role in normal bladder epithelial physiology, possibly in regulating membrane permeability of superficial umbrella cells or in stabilizing the apical membrane through AUM/cytoskeletal interactions. The use of alternate polyadenylation sites has been found for this gene. [provided by RefSeq, Jul 2008]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.36

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.36LOEUF

pLI 0.000

Z-score 0.53

OE 0.85 (0.56–1.36)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.00Z-score

OE missense 1.00 (0.87–1.15)

145 obs / 145.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.85 (0.56–1.36)

0≤0.351.4

Missense OE?1.00 (0.87–1.15)

0≤0.61.4

Synonymous OE?0.65

0≤1.21.6

LoF obs/exp: 13 / 15.2Missense obs/exp: 145 / 145.0Syn Z: 1.98

Background carrier burden — how many people carry a rare variant somewhere in UPK1B?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 160

336 rare PASS variants

Rare truncating (LoF)

1 in 2,200

61 rare PASS variants

Rare synonymous (reference)

1 in 840

91 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for UPK1B. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 210	1 in 2,500
South Asian	~43k	1 in 140	1 in 1,500
Remaining (unassigned)	~30k	1 in 160	1 in 1,800
European (Finnish)	~27k	1 in 1,600	≈ 1 in 13,000
Admixed American	~22k	1 in 110	1 in 1,100
African / African American	~21k	1 in 210	1 in 3,100
East Asian	~20k	1 in 95	≈ 1 in 5,000
Ashkenazi Jewish	~13k	1 in 820	≈ 1 in 4,400
Middle Eastern	~2,884	1 in 97	≈ 1 in 720

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 7 coding exons well covered in gnomAD exomes and genomes.? see exons ↓