UPK2

uroplakin 2

Basic information

Region (hg38): 11:118925164-118958559

Links

ENSG00000110375 ∙ NCBI:7379 ∙ OMIM:611558 ∙ HGNC:12579 ∙ Uniprot:O00526 ∙ 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 UPK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UPK2 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			9		1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding						0
Total	0	0	9	1	1

Variants in UPK2

This is a list of pathogenic ClinVar variants found in the UPK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-118956372-C-T		not specified	Uncertain significance (Dec 22, 2023)
11-118956919-C-T		not specified	Uncertain significance (Oct 29, 2024)
11-118956928-C-T		not specified	Uncertain significance (Dec 19, 2022)
11-118956960-C-A		not specified	Uncertain significance (Jul 28, 2021)
11-118957000-C-T		not specified	Uncertain significance (Jan 03, 2024)
11-118957207-G-A			Likely benign (Jun 20, 2018)
11-118957240-C-T		not specified	Uncertain significance (Oct 22, 2021)
11-118957277-G-A			Benign (Dec 31, 2019)
11-118957303-A-C		not specified	Uncertain significance (Mar 19, 2024)
11-118958106-T-C		not specified	Uncertain significance (Apr 12, 2024)
11-118958225-C-T		not specified	Uncertain significance (Aug 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UPK2	protein_coding	protein_coding	ENST00000264031	5	33397

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.99e-8	0.0500	125295	3	448	125746	0.00179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.237	118	111	1.06	0.00000622	1147
Missense in Polyphen		55	51.947	1.0588		528
Synonymous	-0.187	48	46.4	1.03	0.00000232	439
Loss of Function	-0.916	10	7.32	1.37	4.75e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00338	0.00338
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00310	0.00310
Finnish	0.00	0.00
European (Non-Finnish)	0.00202	0.00201
Middle Eastern	0.00310	0.00310
South Asian	0.00327	0.00317
Other	0.000490	0.000489

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 regulating the assembly of the AUM (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.157

Intolerance Scores

• loftool: 0.827
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.363
• hipred: N
• hipred_score: 0.144
• ghis: 0.393

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.751

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Upk2
• Phenotype: renal/urinary system phenotype; growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype

Gene ontology

• Biological process: multicellular organism development;epithelial cell differentiation
• Cellular component: integral component of plasma membrane;apical plasma membrane;extracellular exosome
• Molecular function: protein binding