PRCC

protein-coding

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

Gene summary

This gene encodes a protein that may play a role in pre-mRNA splicing. Chromosomal translocations (X;1)(p11;q21) that result in fusion of this gene to TFE3 (GeneID 7030) have been associated with papillary renal cell carcinoma. A PRCC-TFE3 fusion protein is expressed in affected carcinomas and is likely associated with altered gene transactivation. This fusion protein has also been associated with disruption of the cell cycle.[provided by RefSeq, Aug 2010]

MANE transcript

NM_005973.5

Inheritance

—

ClinVar variants

U:76B:2

Top phenotype

Papillary renal cell carcinoma type 1

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr1:156,750,610-156,800,815

External References & Databases

Ensembl (ENSG00000143294)

Transcript & Mutation Effects

hg38 • Region Span ~50.2 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 PRCC variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 60

Papillary renal cell carcinoma type 1Total: 3

not providedTotal: 1

YOLK SAC TUMOR AND HIGH-GRADE IMMATURE TERATOMATotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005973.5. 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			2 clinvar			2
missense			68 clinvar	2 clinvar		70
nonsense			3 clinvar			3
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	76	2	0	78

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005973.5	RefSeq	NP_005964.3	7	MANE Select
ENST00000271526.9	Ensembl	ENSP00000271526.4	7	MANE Select
ENST00000454659.1	Ensembl	ENSP00000403560.1	6	Standard
ENST00000526188.5	Ensembl	ENSP00000434762.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

mRNA splicing, via spliceosome
mitotic cell cycle checkpoint

Molecular Function

protein binding

Cellular Component

nucleus
nucleoplasm
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000271526
Coding exons: 7
Length: 50206
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125743
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.09	227	278	0.816	0.0000143	3113
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May regulate cell cycle progression through interaction with MAD2L2. {ECO:0000269|PubMed:11717438}.;

Recessive Scores

pRec: 0.170

Intolerance Scores

LoFtool: 0.116
RVIS EVS: -0.47
RVIS percentile EVS: 23.25

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.955

Gene Damage Prediction

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