URGCP

upregulator of cell proliferation

Basic information

Region (hg38): 7:43875894-43926411

Links

ENSG00000106608 ∙ NCBI:55665 ∙ OMIM:610337 ∙ HGNC:30890 ∙ Uniprot:Q8TCY9 ∙ 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 URGCP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the URGCP 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					7	7
missense			29	3	1	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	8

Variants in URGCP

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

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

Position	Type	Phenotype	Significance	ClinVar
7-43876674-C-T		not specified	Uncertain significance (Feb 23, 2023)
7-43876690-T-G		not specified	Uncertain significance (May 07, 2024)
7-43876814-G-A			Benign (Dec 04, 2018)
7-43876825-C-T		not specified	Uncertain significance (Jan 24, 2024)
7-43876891-C-A		not specified	Uncertain significance (Mar 17, 2023)
7-43876947-A-G		not specified	Uncertain significance (Dec 10, 2024)
7-43877019-T-C		not specified	Uncertain significance (Mar 27, 2023)
7-43877037-G-A		not specified	Uncertain significance (Jun 03, 2024)
7-43877109-G-A		not specified	Uncertain significance (Mar 01, 2024)
7-43877115-T-C		not specified	Uncertain significance (Apr 12, 2022)
7-43877178-G-A		not specified	Uncertain significance (Dec 09, 2024)
7-43877183-G-A			Benign (Dec 04, 2018)
7-43877324-A-C		not specified	Uncertain significance (Sep 02, 2024)
7-43877371-C-T		not specified	Uncertain significance (Nov 17, 2022)
7-43877449-C-T		not specified	Uncertain significance (May 09, 2023)
7-43877454-A-G		not specified	Likely benign (Jan 24, 2023)
7-43877538-C-T		not specified	Uncertain significance (May 17, 2023)
7-43877660-G-A			Benign (Apr 16, 2018)
7-43877710-G-A		not specified	Uncertain significance (Oct 26, 2022)
7-43877724-G-T		not specified	Uncertain significance (Sep 09, 2024)
7-43877735-C-T			Benign (Dec 04, 2018)
7-43877744-G-T			Benign (Apr 20, 2018)
7-43877818-G-C		not specified	Uncertain significance (Apr 30, 2024)
7-43877841-C-A		not specified	Uncertain significance (Dec 12, 2023)
7-43877842-C-T		not specified	Likely benign (Apr 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
URGCP	protein_coding	protein_coding	ENST00000453200	6	50518

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.578	0.422	124784	0	13	124797	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.32	390	542	0.720	0.0000331	6080
Missense in Polyphen		108	193.62	0.55781		2303
Synonymous	0.953	212	230	0.920	0.0000153	1895
Loss of Function	4.22	7	33.3	0.210	0.00000184	364

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000534	0.0000530
Middle Eastern	0.000111	0.000111
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in cell cycle progression through the regulation of cyclin D1 expression. May participate in the development of hepatocellular carcinoma (HCC) by promoting hepatocellular growth and survival. May play an important role in development of gastric cancer. {ECO:0000269|PubMed:12082552, ECO:0000269|PubMed:17217616}.

Intolerance Scores

• loftool: 0.357
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.8

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.443
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Urgcp

Gene ontology

• Biological process: cell cycle
• Cellular component: nucleus;cytosol
• Molecular function: GTP binding