URI1

protein-coding

URI1 prefoldin like chaperone, the group of Prefoldin subunits|Protein phosphatase 1 regulatory subunits

Gene summary

This gene encodes member of the prefoldin family of molecular chaperones. The encoded protein functions as a scaffolding protein and plays roles in ubiquitination and transcription, in part though interactions with the RNA polymerase II subunit RPB5. This gene may play a role in multiple malignancies including ovarian cancer and hepatocellular carcinoma. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 22. [provided by RefSeq, Nov 2011]

Previous symbols:

C19orf2

MANE transcript

NM_003796.3

Inheritance

—

ClinVar variants

U:94B:12

Top phenotype

Abnormality of neuronal migration

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr19:29,923,644-30,016,612

External References & Databases

Ensembl (ENSG00000105176)

Transcript & Mutation Effects

hg38 • Region Span ~93.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to URI1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 90

not providedTotal: 8

Abnormality of neuronal migrationTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003796.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				8 clinvar	1 clinvar	9
missense			92 clinvar	2 clinvar	1 clinvar	95
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	94	10	2	106

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003796.3	RefSeq	NP_003787.2	11	MANE Select
ENST00000392271.6	Ensembl	ENSP00000376097.2	11	MANE Select
NM_001252641.2	RefSeq	NP_001239570.1	11	Standard
ENST00000360605.8	Ensembl	ENSP00000353817.4	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
regulation of cell growth
regulation of transcription by RNA polymerase II
response to virus
negative regulation of phosphatase activity

Molecular Function

RNA polymerase II complex binding
chromatin binding
transcription corepressor activity
protein phosphatase inhibitor activity
protein binding

Cellular Component

nucleus
nucleoplasm
cytoplasm
mitochondrion
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000542441
Coding exons: 11
Length: 92061
Individuals with no LoFs: 125672
Homozygous LoFs: 0
Heterozygous LoFs: 76
Defined: 125748
p: 0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.131	293	287	1.02	0.0000150	3538
Missense (PolyPhen)		63	72.117	0.87357		948
Synonymous	-0.608	113	105	1.08	0.00000597	984
Loss of Function	2.67	13	28.4	0.458	0.00000188	316

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00038	0.00037	rare
Latino/Admixed American	0.00019	0.00017	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00039	0.00038	rare
Finnish	0.00033	0.00032	rare
European (Non-Finnish)	0.00036	0.00034	rare
South Asian	0.00028	0.00026	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in gene transcription regulation. Acts as a transcriptional repressor in concert with the corepressor UXT to regulate androgen receptor (AR) transcription. May act as a tumor suppressor to repress AR-mediated gene transcription and to inhibit anchorage-independent growth in prostate cancer cells. Required for cell survival in ovarian cancer cells. Together with UXT, associates with chromatin to the NKX3-1 promoter region. Antagonizes transcriptional modulation via hepatitis B virus X protein.;

Recessive Scores

pRec: 0.126

Intolerance Scores

RVIS EVS: -0.51
RVIS percentile EVS: 21.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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