UPK3A

uroplakin 3A

Basic information

Region (hg38): 22:45284949-45295874

Previous symbols: [ "UPK3" ]

Links

ENSG00000100373 ∙ NCBI:7380 ∙ OMIM:611559 ∙ HGNC:12580 ∙ Uniprot:O75631 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• renal agenesis, unilateral (Supportive), mode of inheritance: AD
• renal dysplasia (Limited), mode of inheritance: AD
• congenital anomaly of kidney and urinary tract (Disputed Evidence), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Renal/urogenital adysplasia	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary; Renal	15888565
The condition has been described as involving progressive, inexorable renal failure, and renal transplant has been described

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UPK3A gene.

• not_specified (44 variants)
• Renal_hypodysplasia/aplasia_1 (28 variants)
• not_provided (19 variants)
• UPK3A-related_disorder (14 variants)
• Congenital_anomalies_of_kidney_and_urinary_tract_1 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UPK3A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006953.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	6	1	10
missense			53	7	1	61
nonsense			1	2		3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)		1	1	1		3
Total	0	1	58	16	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UPK3A	protein_coding	protein_coding	ENST00000216211	6	10893

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.08e-10	0.0253	123504	20	2224	125748	0.00896

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.411	180	165	1.09	0.00000977	1816
Missense in Polyphen		67	51.783	1.2939		647
Synonymous	0.563	70	76.3	0.918	0.00000515	619
Loss of Function	-0.610	14	11.7	1.19	6.07e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0422	0.0421
Ashkenazi Jewish	0.00327	0.00328
East Asian	0.0274	0.0271
Finnish	0.0271	0.0270
European (Non-Finnish)	0.00189	0.00185
Middle Eastern	0.0274	0.0271
South Asian	0.00116	0.00114
Other	0.00702	0.00686

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}.
• Pathway: Bladder cancer - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0995

Intolerance Scores

• loftool: 0.572
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.14

Haploinsufficiency Scores

• pHI: 0.0786
• hipred: N
• hipred_score: 0.208
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.930

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Upk3a
• Phenotype: homeostasis/metabolism phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: cell morphogenesis;kidney development;water transport;urea transport;epithelial cell differentiation;potassium ion homeostasis;sodium ion homeostasis;urinary bladder development
• Cellular component: endoplasmic reticulum membrane;extracellular exosome;apical plasma membrane urothelial plaque
• Molecular function: protein binding