PRCC

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

Basic information

Region (hg38): 1:156750610-156800815

Links

ENSG00000143294NCBI:5546OMIM:179755HGNC:9343Uniprot:Q92733AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRCC gene.

  • not_specified (51 variants)
  • Papillary_renal_cell_carcinoma_type_1 (3 variants)
  • YOLK_SAC_TUMOR_AND_HIGH-GRADE_IMMATURE_TERATOMA (1 variants)

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. These statistics are base on transcript: NM_000005973.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
53
clinvar
1
clinvar
54
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 53 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PRCCprotein_codingprotein_codingENST00000271526 750206
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9630.0372125741021257430.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.092272780.8160.00001433113
Missense in Polyphen4078.9530.50663898
Synonymous-1.201351181.140.000006561030
Loss of Function3.62219.10.1058.94e-7236

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.000008800.00000879
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Prcc
Phenotype

Gene ontology

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