UPK3B

uroplakin 3B

Basic information

Region (hg38): 7:76510524-76516522

Links

ENSG00000243566 ∙ NCBI:105375355 ∙ OMIM:611887 ∙ HGNC:21444 ∙ Uniprot:Q9BT76 ∙ 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 UPK3B gene.

• Inborn genetic diseases (19 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UPK3B 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			3	1		4
missense			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	1		5
Total	0	0	16	3	0

Variants in UPK3B

This is a list of pathogenic ClinVar variants found in the UPK3B region.

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

Position	Type	Phenotype	Significance	ClinVar
7-76510750-C-A		not specified	Uncertain significance (Apr 22, 2022)
7-76510761-G-T		not specified	Uncertain significance (Dec 01, 2022)
7-76510812-T-C		not specified	Uncertain significance (Jul 12, 2022)
7-76510821-G-A		not specified	Likely benign (Oct 21, 2021)
7-76510888-C-A		not specified	Uncertain significance (Aug 15, 2023)
7-76510918-C-T		not specified	Uncertain significance (Jul 09, 2021)
7-76510930-C-T		not specified	Uncertain significance (Mar 20, 2023)
7-76511034-G-A		not specified	Uncertain significance (Jan 09, 2024)
7-76511663-G-A		not specified	Uncertain significance (Jul 26, 2021)
7-76511734-A-G		not specified	Uncertain significance (Feb 14, 2024)
7-76511744-C-T		not specified	Uncertain significance (Apr 08, 2022)
7-76511797-G-A		not specified	Uncertain significance (Feb 06, 2024)
7-76511803-G-A		not specified	Uncertain significance (Feb 15, 2023)
7-76511855-C-T		not specified	Uncertain significance (Nov 08, 2022)
7-76511879-A-G		not specified	Uncertain significance (Sep 22, 2022)
7-76513957-C-T		not specified	Uncertain significance (Nov 15, 2021)
7-76513971-C-T		not specified	Likely benign (Jan 16, 2024)
7-76513977-C-T		not specified	Likely benign (Feb 27, 2024)
7-76514003-G-A		not specified	Likely benign (Dec 18, 2023)
7-76514032-C-T		not specified	Uncertain significance (Jan 29, 2024)
7-76514065-T-C		not specified	Likely benign (Jan 01, 2023)
7-76514072-C-T		not specified	Uncertain significance (Jan 09, 2024)
7-76514074-C-T		not specified	Uncertain significance (Nov 06, 2023)
7-76515074-C-T		not specified	Likely benign (Mar 01, 2024)
7-76515075-G-A		not specified	Likely benign (Nov 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UPK3B	protein_coding	protein_coding	ENST00000419923	4	508596

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000234	0.771	123747	0	38	123785	0.000153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.193	177	184	0.960	0.0000117	1954
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000178
Ashkenazi Jewish	0.00	0.00
East Asian	0.00100	0.000929
Finnish	0.00	0.00
European (Non-Finnish)	0.000119	0.000107
Middle Eastern	0.00100	0.000929
South Asian	0.00	0.00
Other	0.000534	0.000498

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 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

Haploinsufficiency Scores

• pHI: 0.0772
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00904

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Upk3b

Zebrafish Information Network

• Gene name: upk3b
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: negative regulation of gene expression
• Cellular component: plasma membrane;integral component of membrane