UPK1A

uroplakin 1A, the group of Tetraspanins

Basic information

Region (hg38): 19:35666517-35678481

Links

ENSG00000105668 ∙ NCBI:11045 ∙ OMIM:611557 ∙ HGNC:12577 ∙ Uniprot:O00322 ∙ 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 UPK1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UPK1A 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			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	0	0

Variants in UPK1A

This is a list of pathogenic ClinVar variants found in the UPK1A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35666817-C-T		not specified	Uncertain significance (Sep 09, 2024)
19-35666846-G-A		not specified	Uncertain significance (Feb 10, 2023)
19-35668467-C-G		not specified	Uncertain significance (Oct 26, 2021)
19-35668475-G-A		not specified	Uncertain significance (Sep 09, 2024)
19-35668476-C-T		not specified	Uncertain significance (Sep 09, 2024)
19-35668486-A-G		not specified	Uncertain significance (Dec 13, 2023)
19-35668499-G-A		not specified	Uncertain significance (Aug 20, 2024)
19-35668559-G-T		not specified	Uncertain significance (Dec 22, 2023)
19-35668565-A-G		not specified	Uncertain significance (Jul 07, 2022)
19-35668580-G-A		not specified	Uncertain significance (Apr 01, 2024)
19-35668590-T-C		not specified	Uncertain significance (Jan 07, 2022)
19-35668632-G-A		not specified	Uncertain significance (Sep 22, 2022)
19-35668640-T-C		not specified	Uncertain significance (Dec 12, 2023)
19-35668653-C-T		not specified	Uncertain significance (Mar 31, 2023)
19-35673295-C-T		not specified	Uncertain significance (Jan 22, 2025)
19-35673298-C-A		not specified	Uncertain significance (Aug 20, 2024)
19-35673488-C-G		not specified	Uncertain significance (Jan 24, 2024)
19-35673538-T-C		not specified	Uncertain significance (Aug 28, 2024)
19-35675868-T-C		not specified	Uncertain significance (Dec 16, 2024)
19-35675886-C-T		not specified	Uncertain significance (Jun 29, 2023)
19-35675898-G-A		not specified	Uncertain significance (Feb 07, 2025)
19-35675904-C-A		not specified	Uncertain significance (Jun 13, 2023)
19-35675915-G-A		not specified	Uncertain significance (Mar 14, 2023)
19-35675952-C-T		not specified	Uncertain significance (Jun 18, 2021)
19-35675972-A-C		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UPK1A	protein_coding	protein_coding	ENST00000222275	7	11653

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.21e-11	0.0383	125674	1	73	125748	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0531	176	174	1.01	0.0000106	1673
Missense in Polyphen		53	57.664	0.91912		569
Synonymous	0.358	66	69.8	0.946	0.00000467	517
Loss of Function	-0.254	15	14.0	1.07	6.07e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000322	0.000322
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.000163	0.000163
South Asian	0.00134	0.00127
Other	0.000163	0.000163

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: 0.0946

Intolerance Scores

• loftool: 0.506
• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.79

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.275
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.586

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Upk1a

Gene ontology

• Biological process: cell surface receptor signaling pathway;epithelial cell differentiation;protein complex oligomerization
• Cellular component: endoplasmic reticulum;plasma membrane;integral component of plasma membrane;cell surface;integral component of membrane;extracellular exosome;apical plasma membrane urothelial plaque
• Molecular function: protein binding;protein homodimerization activity