PRCC

proline rich mitotic checkpoint control factor, the group of Spliceosomal Bact complex

Basic information

Region (hg38): 1:156750610-156800815

Links

ENSG00000143294 ∙ NCBI:5546 ∙ OMIM:179755 ∙ HGNC:9343 ∙ Uniprot:Q92733 ∙ 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 PRCC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRCC 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in PRCC

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

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

Position	Type	Phenotype	Significance	ClinVar
1-156752232-A-T		not specified	Likely benign (Sep 28, 2021)
1-156767831-G-T		not specified	Uncertain significance (May 23, 2024)
1-156767832-C-G		not specified	Uncertain significance (Dec 14, 2023)
1-156767833-C-T		not specified	Uncertain significance (Oct 20, 2024)
1-156767868-C-T		not specified	Uncertain significance (May 17, 2023)
1-156767925-C-T		not specified	Uncertain significance (Jun 05, 2024)
1-156767994-C-A		not specified	Uncertain significance (Jan 22, 2024)
1-156768016-C-T		not specified	Uncertain significance (Aug 27, 2024)
1-156768133-A-G		not specified	Likely benign (May 30, 2024)
1-156768228-C-G		not specified	Uncertain significance (Oct 17, 2023)
1-156786657-A-G		not specified	Uncertain significance (Sep 09, 2024)
1-156786693-C-G		not specified	Uncertain significance (Feb 10, 2023)
1-156786714-C-A		not specified	Uncertain significance (Feb 12, 2024)
1-156786717-C-T		not specified	Uncertain significance (Sep 28, 2021)
1-156786731-G-C		not specified	Uncertain significance (Sep 14, 2022)
1-156786766-G-C		not specified	Uncertain significance (Dec 21, 2023)
1-156786792-G-T		not specified	Uncertain significance (Jun 04, 2024)
1-156786810-C-T		not specified	Uncertain significance (May 14, 2024)
1-156786813-C-T		Papillary renal cell carcinoma type 1	Uncertain significance (Jun 07, 2022)
1-156786911-G-A		not specified	Uncertain significance (Jun 22, 2021)
1-156786926-C-T		not specified	Uncertain significance (Sep 26, 2023)
1-156786947-C-G		not specified	Uncertain significance (Jan 07, 2022)
1-156786999-C-T		YOLK SAC TUMOR AND HIGH-GRADE IMMATURE TERATOMA	other (May 01, 2016)
1-156787034-G-A		not specified	Uncertain significance (Oct 25, 2024)
1-156787089-C-G		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRCC	protein_coding	protein_coding	ENST00000271526	7	50206

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.963	0.0372	125741	0	2	125743	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	227	278	0.816	0.0000143	3113
Missense in Polyphen		40	78.953	0.50663		898
Synonymous	-1.20	135	118	1.14	0.00000656	1030
Loss of Function	3.62	2	19.1	0.105	8.94e-7	236

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate cell cycle progression through interaction with MAD2L2. {ECO:0000269|PubMed:11717438}.
• Pathway: Renal cell carcinoma - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Type 2 papillary renal cell carcinoma;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.170

Intolerance Scores

• loftool: 0.116
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.332
• hipred: Y
• hipred_score: 0.729
• ghis: 0.596

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prcc

Gene ontology

• Biological process: mRNA splicing, via spliceosome;mitotic cell cycle checkpoint
• Cellular component: nucleus;nucleoplasm;nuclear speck
• Molecular function: protein binding