UPK1B

uroplakin 1B, the group of Tetraspanins

Basic information

Region (hg38): 3:119173517-119205143

Previous symbols: [ "UPK1" ]

Links

ENSG00000114638 ∙ NCBI:7348 ∙ OMIM:602380 ∙ HGNC:12578 ∙ Uniprot:O75841 ∙ 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 UPK1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UPK1B 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in UPK1B

This is a list of pathogenic ClinVar variants found in the UPK1B region.

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

Position	Type	Phenotype	Significance	ClinVar
3-119186767-G-A		not specified	Uncertain significance (Oct 03, 2023)
3-119187781-G-A		not specified	Uncertain significance (Dec 20, 2023)
3-119187797-C-T		not specified	Uncertain significance (Jan 04, 2022)
3-119187835-T-C		not specified	Uncertain significance (Apr 08, 2022)
3-119187889-G-A		not specified	Uncertain significance (Jan 26, 2025)
3-119187944-T-A		not specified	Uncertain significance (Dec 09, 2024)
3-119187948-G-C		not specified	Uncertain significance (Feb 14, 2025)
3-119187971-T-G		not specified	Uncertain significance (Jan 10, 2025)
3-119187974-C-T		not specified	Uncertain significance (Apr 06, 2022)
3-119190255-T-C		not specified	Uncertain significance (Jan 19, 2024)
3-119190267-T-C		not specified	Uncertain significance (Jan 26, 2022)
3-119190303-C-G		not specified	Uncertain significance (Jul 26, 2024)
3-119190989-C-T		not specified	Uncertain significance (Dec 16, 2024)
3-119191082-C-T		not specified	Uncertain significance (Jun 09, 2022)
3-119194251-C-G		not specified	Uncertain significance (Mar 31, 2024)
3-119194312-C-G		not specified	Uncertain significance (Dec 10, 2024)
3-119194331-A-G		not specified	Uncertain significance (May 24, 2023)
3-119194366-A-C		not specified	Uncertain significance (Feb 07, 2025)
3-119199073-T-A		not specified	Uncertain significance (Jan 02, 2025)
3-119199084-A-G		not specified	Uncertain significance (Feb 18, 2025)
3-119199091-G-A		not specified	Uncertain significance (Feb 19, 2025)
3-119203933-G-A		not specified	Uncertain significance (Nov 19, 2024)
3-119203944-T-C		not specified	Uncertain significance (Nov 17, 2023)
3-119203957-T-C		not specified	Uncertain significance (Oct 02, 2023)
3-119203959-G-A		not specified	Uncertain significance (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UPK1B	protein_coding	protein_coding	ENST00000264234	7	31637

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.18e-8	0.268	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.000674	145	145	1.00	0.00000748	1730
Missense in Polyphen		55	52.154	1.0546		645
Synonymous	1.98	34	52.2	0.651	0.00000286	476
Loss of Function	0.530	13	15.2	0.853	7.37e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000618	0.000618
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000238	0.000237
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.000653	0.000652

dbNSFP

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 normal bladder epithelial physiology, possibly in regulating membrane permeability of superficial umbrella cells or in stabilizing the apical membrane through AUM/cytoskeletal interactions (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.620
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.350
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.711

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Upk1b
• Phenotype: normal phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway;response to bacterium;epithelial cell differentiation
• Cellular component: integral component of plasma membrane;integral component of membrane;extracellular exosome;apical plasma membrane urothelial plaque
• Molecular function: structural molecule activity