UPK1A

uroplakin 1A, the group of Tetraspanins

Basic information

Region (hg38): 19:35666517-35678481

Links

ENSG00000105668NCBI:11045OMIM:611557HGNC:12577Uniprot:O00322AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
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)3466277
19-35666846-G-A not specified Uncertain significance (Feb 10, 2023)2467847
19-35668467-C-G not specified Uncertain significance (Oct 26, 2021)2368635
19-35668475-G-A not specified Uncertain significance (Sep 09, 2024)3466273
19-35668476-C-T not specified Uncertain significance (Sep 09, 2024)3466275
19-35668486-A-G not specified Uncertain significance (Dec 13, 2023)3186791
19-35668499-G-A not specified Uncertain significance (Aug 20, 2024)3466278
19-35668559-G-T not specified Uncertain significance (Dec 22, 2023)3186792
19-35668565-A-G not specified Uncertain significance (Jul 07, 2022)2300004
19-35668580-G-A not specified Uncertain significance (Apr 01, 2024)3331150
19-35668590-T-C not specified Uncertain significance (Jan 07, 2022)2270688
19-35668632-G-A not specified Uncertain significance (Sep 22, 2022)2213130
19-35668640-T-C not specified Uncertain significance (Dec 12, 2023)3186793
19-35668653-C-T not specified Uncertain significance (Mar 31, 2023)2531878
19-35673298-C-A not specified Uncertain significance (Aug 20, 2024)3466280
19-35673488-C-G not specified Uncertain significance (Jan 24, 2024)3186794
19-35673538-T-C not specified Uncertain significance (Aug 28, 2024)2356005
19-35675886-C-T not specified Uncertain significance (Jun 29, 2023)2603221
19-35675898-G-A not specified Uncertain significance (Oct 26, 2022)3186795
19-35675904-C-A not specified Uncertain significance (Jun 13, 2023)2560096
19-35675915-G-A not specified Uncertain significance (Mar 14, 2023)3186796
19-35675952-C-T not specified Uncertain significance (Jun 18, 2021)2365098
19-35675972-A-C not specified Uncertain significance (Aug 08, 2022)2251722
19-35675988-G-T not specified Uncertain significance (Oct 16, 2024)3466279
19-35676003-A-T not specified Uncertain significance (Sep 17, 2021)2251228

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
UPK1Aprotein_codingprotein_codingENST00000222275 711653
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
7.21e-110.03831256741731257480.000294
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.05311761741.010.00001061673
Missense in Polyphen5357.6640.91912569
Synonymous0.3586669.80.9460.00000467517
Loss of Function-0.2541514.01.076.07e-7144

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003220.000322
Ashkenazi Jewish0.00009940.0000992
East Asian0.0001630.000163
Finnish0.000.00
European (Non-Finnish)0.0001770.000176
Middle Eastern0.0001630.000163
South Asian0.001340.00127
Other0.0001630.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Upk1a
Phenotype

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