PRCC

Summary

PRCC (proline rich mitotic checkpoint control factor, HGNC:9343) is a protein-coding gene on chromosome 1q23.1, encoding Proline-rich protein PRCC (Q92733). May regulate cell cycle progression through interaction with MAD2L2. It is a selective cancer dependency (DepMap: 20.9% of cell lines).

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.

Source: NCBI Gene 5546 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 83 total
• GTEx eGene: eQTL in 9 tissues, sQTL in 19 (q < 0.05)
• Phenotypes (HPO): 4
• Cancer dependency (DepMap): dependent in 20.9% of screened cell lines
• Constraint (gnomAD): pLI 1.00 (loss-of-function intolerant), LOEUF 0.40 (moderately constrained)
• MANE Select transcript: NM_005973
• Notable: 83 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9343
Approved symbol	PRCC
Name	proline rich mitotic checkpoint control factor
Location	1q23.1
Locus type	gene with protein product
Status	Approved
Aliases	RCCP1
Ensembl gene	ENSG00000143294
Ensembl biotype	protein_coding
OMIM	179755
Entrez	5546

Gene structure

Transcript identifiers

Ensembl transcripts: 38 — 22 protein_coding, 12 nonsense_mediated_decay, 2 retained_intron, 2 protein_coding_CDS_not_defined

MANE Select: ENST00000271526

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 4, TSL 3: 2

ENST00000271526, ENST00000454659, ENST00000459707, ENST00000469071, ENST00000473387, ENST00000491853, ENST00000526188, ENST00000888086, ENST00000888087, ENST00000888088, ENST00000888089, ENST00000888090, ENST00000888091, ENST00000888092, ENST00000927762, ENST00000927763, ENST00000927764, ENST00000927765, ENST00000927766, ENST00000927767, ENST00000927768, ENST00000927769, ENST00000950490, ENST00000950491, ENST00000950492, ENST00000998797, ENST00000998798, ENST00000998799, ENST00000998800, ENST00001052644, ENST00001070776, ENST00001070777, ENST00001070779, ENST00001070780, ENST00001070781, ENST00001070782, ENST00001070783, ENST00001144567

RefSeq mRNA: 1 — MANE Select: NM_005973 NM_005973

CCDS: CCDS1157

Canonical transcript exons

ENST00000271526 — 7 exons

Exon	Start	End
ENSE00000959080	156794665	156794808
ENSE00000959081	156797276	156797341
ENSE00001833466	156767535	156768239
ENSE00001870245	156800374	156800815
ENSE00003510161	156786608	156787174
ENSE00003525835	156782282	156782329
ENSE00003607660	156791697	156791792

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 96.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 57.7872 / max 357.8567, expressed in 1821 samples.

Highest expression (Bgee): cortical plate, ganglionic eminence, ventricular zone, cerebellar hemisphere, hemisphere of cerebellum.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PRCC is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 9 tissues and its splicing (sQTL) in 19 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 28 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Skin Sun Exposed Lower leg	sqtl	6.3e-16	+0.48	1:156795125:G:A
Cells EBV-transformed lymphocytes	sqtl	4.2e-12	+0.64	1:156805287:C:T
Testis	sqtl	2.5e-11	+0.62	1:156792126:C:G
Artery Tibial	sqtl	1.5e-10	+0.44	1:156791095:C:A
Lung	sqtl	2.2e-10	+0.44	1:156791095:C:A
Esophagus Mucosa	sqtl	1.1e-09	+0.51	1:156765620:G:A
Skin Not Sun Exposed Suprapubic	sqtl	4.4e-09	+0.43	1:156791095:C:A
Breast Mammary Tissue	sqtl	3.9e-08	+0.48	1:156791095:C:A
Thyroid	sqtl	1.4e-07	+0.41	1:156765620:G:A
Cells Cultured fibroblasts	sqtl	1.7e-07	+0.44	1:156765620:G:A
Adipose Subcutaneous	sqtl	6.3e-07	+0.38	1:156791095:C:A
Whole Blood	sqtl	9.4e-07	+0.37	1:156792126:C:G
Stomach	sqtl	5.3e-05	+0.44	1:156765620:G:A
Colon Transverse	sqtl	6.0e-05	+0.39	1:156791095:C:A
Pancreas	eqtl	1.4e-04	-0.24	1:156806925:T:C
Artery Aorta	sqtl	4.5e-04	+0.39	1:156795125:G:A
Brain Cerebellum	sqtl	1.2e-03	+0.58	1:156765620:G:A
Brain Anterior cingulate cortex BA24	eqtl	2.3e-03	-2.40	1:155921164:G:A
Skin Not Sun Exposed Suprapubic	eqtl	3.8e-03	-0.08	1:156728473:C:T
Thyroid	eqtl	6.7e-03	+0.43	1:156756011:G:A

FANTOM5 promoters

6 alternative TSS:

Promoter ID	TPM avg	Samples expressed
5775	56.8173	1820
5776	0.3372	152
5777	0.2468	83
5771	0.1953	99
5774	0.1310	31
5773	0.0597	10

Top tissues by expression

showing 100 of 298 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	96.92	gold quality
ganglionic eminence	UBERON:0004023	96.53	gold quality
ventricular zone	UBERON:0003053	95.57	gold quality
cerebellar hemisphere	UBERON:0002245	95.26	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.26	gold quality
cerebellar cortex	UBERON:0002129	95.17	gold quality
right frontal lobe	UBERON:0002810	94.99	gold quality
skin of leg	UBERON:0001511	94.95	gold quality
right lobe of thyroid gland	UBERON:0001119	94.83	gold quality
skin of abdomen	UBERON:0001416	94.82	gold quality
hindlimb stylopod muscle	UBERON:0004252	94.82	gold quality
gastrocnemius	UBERON:0001388	94.78	gold quality
stromal cell of endometrium	CL:0002255	94.61	gold quality
mucosa of transverse colon	UBERON:0004991	94.56	gold quality
muscle layer of sigmoid colon	UBERON:0035805	94.35	gold quality
left lobe of thyroid gland	UBERON:0001120	94.32	gold quality
body of uterus	UBERON:0009853	94.23	gold quality
apex of heart	UBERON:0002098	94.20	gold quality
lower esophagus mucosa	UBERON:0035834	94.16	gold quality
muscle of leg	UBERON:0001383	94.14	gold quality
granulocyte	CL:0000094	94.11	gold quality
right lung	UBERON:0002167	94.10	gold quality
endocervix	UBERON:0000458	94.02	gold quality
ectocervix	UBERON:0012249	93.96	gold quality
lower esophagus muscularis layer	UBERON:0035833	93.93	gold quality
left uterine tube	UBERON:0001303	93.92	gold quality
lower esophagus	UBERON:0013473	93.92	gold quality
right ovary	UBERON:0002118	93.85	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	93.83	gold quality
prefrontal cortex	UBERON:0000451	93.77	gold quality
cerebellum	UBERON:0002037	93.75	gold quality
rectum	UBERON:0001052	93.74	gold quality
adenohypophysis	UBERON:0002196	93.71	gold quality
popliteal artery	UBERON:0002250	93.66	gold quality
tibial artery	UBERON:0007610	93.66	gold quality
gall bladder	UBERON:0002110	93.65	gold quality
islet of Langerhans	UBERON:0000006	93.56	gold quality
upper lobe of left lung	UBERON:0008952	93.55	gold quality
esophagus	UBERON:0001043	93.53	gold quality
small intestine Peyer’s patch	UBERON:0003454	93.53	gold quality
body of stomach	UBERON:0001161	93.46	gold quality
left ovary	UBERON:0002119	93.44	gold quality
cingulate cortex	UBERON:0003027	93.41	gold quality
anterior cingulate cortex	UBERON:0009835	93.36	gold quality
spleen	UBERON:0002106	93.34	gold quality
minor salivary gland	UBERON:0001830	93.33	gold quality
thyroid gland	UBERON:0002046	93.30	gold quality
esophagus mucosa	UBERON:0002469	93.28	gold quality
tibial nerve	UBERON:0001323	93.23	gold quality
descending thoracic aorta	UBERON:0002345	93.22	gold quality
right uterine tube	UBERON:0001302	93.18	gold quality
transverse colon	UBERON:0001157	93.14	gold quality
aorta	UBERON:0000947	93.10	gold quality
mucosa of stomach	UBERON:0001199	93.08	gold quality
left adrenal gland	UBERON:0001234	93.08	gold quality
right adrenal gland cortex	UBERON:0035827	93.08	gold quality
metanephros cortex	UBERON:0010533	93.07	gold quality
left adrenal gland cortex	UBERON:0035825	93.02	gold quality
left coronary artery	UBERON:0001626	92.98	gold quality
omental fat pad	UBERON:0010414	92.97	gold quality
smooth muscle tissue	UBERON:0001135	92.95	gold quality
peritoneum	UBERON:0002358	92.92	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	92.80	gold quality
upper lobe of lung	UBERON:0008948	92.80	gold quality
right testis	UBERON:0004534	92.74	gold quality
right adrenal gland	UBERON:0001233	92.71	gold quality
body of pancreas	UBERON:0001150	92.68	gold quality
right atrium auricular region	UBERON:0006631	92.63	gold quality
nucleus accumbens	UBERON:0001882	92.60	gold quality
right coronary artery	UBERON:0001625	92.57	gold quality
thoracic aorta	UBERON:0001515	92.54	gold quality
amygdala	UBERON:0001876	92.52	gold quality
ascending aorta	UBERON:0001496	92.50	gold quality
caudate nucleus	UBERON:0001873	92.48	gold quality
left testis	UBERON:0004533	92.38	gold quality
coronary artery	UBERON:0001621	92.24	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	92.23	gold quality
stomach	UBERON:0000945	92.22	gold quality
heart left ventricle	UBERON:0002084	92.21	gold quality
colonic epithelium	UBERON:0000397	92.14	gold quality
right lobe of liver	UBERON:0001114	92.12	gold quality
adrenal gland	UBERON:0002369	92.11	gold quality
adrenal cortex	UBERON:0001235	92.09	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.09	gold quality
zone of skin	UBERON:0000014	92.07	gold quality
pituitary gland	UBERON:0000007	92.06	gold quality
adipose tissue of abdominal region	UBERON:0007808	91.98	gold quality
lymph node	UBERON:0000029	91.90	gold quality
small intestine	UBERON:0002108	91.90	gold quality
putamen	UBERON:0001874	91.80	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.75	gold quality
cardiac ventricle	UBERON:0002082	91.69	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	91.64	gold quality
pancreas	UBERON:0001264	91.63	gold quality
sigmoid colon	UBERON:0001159	91.62	gold quality
cardiac atrium	UBERON:0002081	91.55	gold quality
embryo	UBERON:0000922	91.38	gold quality
testis	UBERON:0000473	91.09	gold quality
mouth mucosa	UBERON:0003729	91.09	gold quality
monocyte	CL:0000576	91.08	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.79
E-GEOD-110499	no	253.81
E-MTAB-8060	no	111.26

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Skeletal muscle	tissue	54.0	low
Postcentral gyrus	tissue	44.0
Corpus callosum	tissue	43.7
Hippocampus	tissue	42.7	not detected
Nucleus accumbens	tissue	42.6
Choroid plexus	tissue	41.2
Bone marrow	tissue	39.6	medium
Superior colliculi	tissue	39.5
Thalamus	tissue	39.4
Midbrain	tissue	39.3
Spinal cord	tissue	38.3
Medulla oblongata	tissue	37.4
Pons	tissue	37.0
Cerebral cortex	tissue	36.2	medium
Locus coeruleus	tissue	36.2
Somatosensory cortex	tissue	36.2
Substantia nigra	tissue	35.8
Hippocampal formation	tissue	35.5
Thymus	tissue	34.9
Cerebellum	tissue	34.8	medium
Frontal cortex	tissue	34.7
Skin 1	tissue	34.6	high
Lymph node	tissue	34.0	medium
Occipital cortex	tissue	33.9
Parathyroid gland	tissue	32.6	high
Caudate putamen	tissue	32.6
Tongue	tissue	32.2
Putamen	tissue	32.1
Hypothalamus	tissue	31.8
Prefrontal cortex	tissue	31.6
Motor cortex	tissue	31.4
Ventral forebrain	tissue	31.4
Vagina	tissue	31.3	high
Periaqueductal gray	tissue	31.2
Spleen	tissue	30.7	low
Basal ganglia	tissue	29.8	not detected
Septum	tissue	29.7
Olfactory bulb	tissue	29.5
Entorhinal cortex	tissue	29.2
Temporal cortex	tissue	29.2
Ovary	tissue	28.8	medium
Retrosplenial and cingulate cortex	tissue	28.8
Retrosplenial cortex	tissue	28.8
Tonsil	tissue	28.7	medium
Salivary gland	tissue	28.6	low
Urinary bladder	tissue	28.6	high
Appendix	tissue	28.0	medium
Pituitary gland	tissue	27.8
Placenta	tissue	27.2	high
Insular cortex	tissue	26.4
Small intestine	tissue	26.0	medium
Endometrium 1	tissue	25.7	low
Amygdala	tissue	25.7
Esophagus	tissue	25.6	medium
Smooth muscle	tissue	25.5	medium
Duodenum	tissue	25.4	medium
Fallopian tube	tissue	25.1	medium
Adipose tissue	tissue	25.0	low
Heart muscle	tissue	24.9	not detected
Thyroid gland	tissue	24.8	high

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Corpus callosum, splenium (white matter) (48.8), Area striata (white matter) (48.7), Parieto-temporal junction (white matter) (48.4), Perirhinal gyrus (47.3), Olfactory area (46.9).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting PRCC by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 31 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-4499	99.62	67.29	1470
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-1207-3P	98.99	66.22	1532
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-421	98.90	67.04	1883
HSA-MIR-29B-1-5P	98.86	68.35	1364
HSA-MIR-7155-5P	98.65	66.14	1290
HSA-MIR-615-5P	98.10	63.76	591
HSA-MIR-6742-3P	97.95	64.50	1490
HSA-MIR-4494	97.86	64.93	850
HSA-MIR-2278	97.30	66.19	1130
HSA-MIR-1225-3P	97.29	64.60	876

Functional genomics

gnomAD constraint: pLI 1, LOEUF 0.403, missense Z 0.452 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000271526 splits into 4 regions with different missense tolerance; 0 are missense-constrained. Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)	Missense obs / exp	o/e	Constrained
1:156,767,772–156,768,200	245 / 188.5	1.30	no
1:156,768,201–156,786,927	118 / 166.7	0.71	no
1:156,786,928–156,791,752	141 / 130.2	1.08	no
1:156,791,753–156,800,457	69 / 139.3	0.50	no
DepMap (CRISPR cell-line fitness): dependent in 20.9% of screened cell lines.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): MDA-MB-361 (-1.268), NB13 (-1.08), MFE-296 (-1.025), KMS-11 (-0.951), CCRF-HSB-2-DM (-0.941), GP5d (-0.935), JM1 (-0.917), MON (-0.914), CHP-212 (-0.9), RS4;11 (-0.896), Raji (-0.874), KARPAS 1718 (-0.857), KML-1 (-0.836), NALM-16 (-0.835), MM426 (-0.831).

Literature-anchored findings (GeneRIF, showing 3)

• Our data suggest a scenario in which, during the course of renal cell carcinoma development, an initial PRCCTFE3-induced cell cycle delay must be numbed, thus permitting continued proliferation and progression towards full-blown malignancy. (PMID:19422821)
• results reveal that PRCC-TFE3 dual-fusion FISH probe is an efficient and concise technique for diagnosing PRCC-TFE3 RCC in paraffin-embedded tissue (PMID:28949976)
• PRCC-TFE3 fusion-mediated PRKN/parkin-dependent mitophagy promotes cell survival and proliferation in PRCC-TFE3 translocation renal cell carcinoma. (PMID:33019842)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	prcc	ENSDARG00000063252
mus_musculus	Prcc	ENSMUSG00000004895
rattus_norvegicus	Prcc	ENSRNOG00000012933
drosophila_melanogaster	CG17249	FBGN0035249
caenorhabditis_elegans		WBGENE00008034

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
HDGF	protein-coding	3068
INSRR	protein-coding	3645
NTRK1	protein-coding	4914
METTL25B	protein-coding	51093
MRPL24	protein-coding	79590
ISG20L2	protein-coding	81875
SH2D2A	protein-coding	9047
LRRC71	protein-coding	149499
PEAR1	protein-coding	375033
MIR765	ncRNA	768220
ARHGEF11	protein-coding	9826
CRABP2	protein-coding	1382
NES	protein-coding	10763

Protein

Protein identifiers

Proline-rich protein PRCC — Q92733 (reviewed: Q92733)

Alternative names: Papillary renal cell carcinoma translocation-associated gene protein

All UniProt accessions (5): A0A0S2Z456, A0A0S2Z483, H0Y679, H0YE12, Q92733

UniProt curated annotations — full annotation on UniProt →

Function. May regulate cell cycle progression through interaction with MAD2L2.

Subunit / interactions. Interacts with MAD2L2; the interaction is direct.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitous in fetal and adult tissues.

Disease relevance. A chromosomal aberration involving PRCC is found in patients with papillary renal cell carcinoma. Translocation t(X;1)(p11.2;q21.2) with TFE3.

RefSeq proteins (1): NP_005964* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018800	PRCC	Family

Pfam: PF10253

UniProt features (22 total): modified residue 9, compositionally biased region 7, region of interest 4, chain 1, sequence variant 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q92733-F1	59.89	0.06

Human Protein Atlas

Protein class: Predicted intracellular proteins, Plasma proteins, Cancer-related genes, Disease related genes, Human disease related genes, Essential proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nuclear speckles

Antibody reliability (HPA): IH supported · IF enhanced

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (9)

Type	Positions
Phosphoserine	97, 114, 157, 159, 212, 218, 241, 267
Phosphothreonine	239

Function

Pathways and Gene Ontology

Reactome pathways

2 curated (TAS) of 5; 1 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

5 pathways:

ID	Pathway	Evidence
R-HSA-9918481	Dengue Virus-Host Interactions ⚕	curated
R-HSA-72163	mRNA Splicing - Major Pathway	curated
R-HSA-8953854	Metabolism of RNA	—
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA	—
R-HSA-72172	mRNA Splicing	—

MSigDB gene sets: 156 (showing top): PATIL_LIVER_CANCER, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_REGULATION_OF_CELL_CYCLE, REACTOME_MRNA_SPLICING, MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_17, TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA, BOYAULT_LIVER_CANCER_SUBCLASS_G12_UP, MODULE_18, MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_24, DURCHDEWALD_SKIN_CARCINOGENESIS_DN, REACTOME_METABOLISM_OF_RNA, TGGAAA_NFAT_Q4_01, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, TCCCRNNRTGC_UNKNOWN

GO Biological Process (1): regulation of cell cycle (GO:0051726)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nuclear speck (GO:0016607)

Reactome top-level categories

4 top-level categories:

Category	Pathways
mRNA Splicing	1
Dengue Virus Infection	1
Processing of Capped Intron-Containing Pre-mRNA	1
Metabolism of RNA	1

GO top-level categories

7 GO namespaces:

Category	Terms
cell cycle	1
regulation of cellular process	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
nuclear ribonucleoprotein granule	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 3 of 5 annotations. The rest are phylogenetic / computational / electronic (IEA).

3 experimentally-supported GO terms:

GO term	NS	Evidence
regulation of cell cycle	BP	direct assay
nuclear speck	CC	direct assay
nucleus	CC	direct assay

Protein interactions and networks

STRING

showing 15 of 746 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRCC	LUC7L3	O95232	649
PRCC	ASPSCR1	Q9BZE9	628
PRCC	TFE3	P19532	602
PRCC	RBM10	P98175	591
PRCC	TPRN	Q4KMQ1	549
PRCC	CDH16	O75309	530
PRCC	PPIL2	Q13356	530
PRCC	KHSRP	Q92945	524
PRCC	NONO	P30807	495
PRCC	MAD2L2	Q9UI95	479
PRCC	TPR	P12270	470
PRCC	CLTC	Q00610	454
PRCC	SNAPC3	Q92966	454
PRCC	TRPC5	Q9UL62	441
PRCC	SFPQ	P23246	420

IntAct

Human interaction partners of PRCC in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

24 partners by confidence:

Partner	Interaction type	MIscore	Records
HOMER3	physical association	0.560	3
NTC20	physical association	0.560	3
EGFR	physical association	0.550	2
BCAS2	association	0.530	2
CSNK2A1	phosphorylation reaction	0.440	1
DNAJC10	physical association	0.400	1
SF3A2	physical association	0.400	1
LSM2	physical association	0.370	1
PPIL2	physical association	0.370	1
PRPF19	physical association	0.370	1
RBM10	physical association	0.370	1
TOE1	physical association	0.370	1
CDK5	physical association	0.000	1
CHORDC1	physical association	0.000	1
COPZ1	physical association	0.000	1
DIS3	physical association	0.000	1
DRG1	physical association	0.000	1
GORASP2	physical association	0.000	1
SARNP	physical association	0.000	1
SCYL2	physical association	0.000	1
SEPTIN11	physical association	0.000	1
SEPTIN7	physical association	0.000	1
SH3GLB1	physical association	0.000	1
SUB1	physical association	0.000	1

BioGRID (126 interactions; top human partners by supporting records): MAD2L2 (Two-hybrid; 4 records), LSM2 (Proximity Label-MS; 3 records), PRPF19 (Proximity Label-MS; 3 records), WRAP73 (Affinity Capture-MS; 3 records), BCAM (Affinity Capture-MS; 2 records), BCAS2 (Affinity Capture-MS; 2 records), C19orf57 (Affinity Capture-MS; 2 records), CARM1 (Affinity Capture-MS; 2 records), CDC5L (Affinity Capture-MS; 2 records), F11 (Affinity Capture-MS; 2 records), FKBP9 (Affinity Capture-MS; 2 records), HSPA9 (Affinity Capture-MS; 2 records), PPIL2 (Two-hybrid; 2 records), RBM10 (Two-hybrid; 2 records), SNRNP40 (Proximity Label-MS; 2 records)

SIGNOR signaling

1 signaling interactions:

A	Effect	B	Mechanism
PRCC	up-regulates	MAD2L2	relocalization

Protein complexes (CORUM) (1)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

1 complexes by size:

Complex	Subunits	Members
Spliceosome, A complex	112	RBM39, SAP30BP, CDK11A, CHERP, HNRNPA1, HNRNPK, HNRNPR, HNRNPU, RBM25, SF3A1, DDX46, HNRNPA3, RNPS1, SART1, SF1, SF3A2, SF3B4, SNRPB, ACIN1, CCAR2, DHX9, ELAVL1, ILF2, SF3B3, SRSF5, HNRNPA2B1, CD2BP2, DDX5, PUF60, RBM17, SNRPA1, TCERG1, ZC3H18, SNRPD1, SRSF2, SYNCRIP, ZNF207, CTNNBL1, HSPA8, NCBP2, SF3B2, TRA2B, YBX1, RBM10, SF3A3, SRRM1, SRSF6, SRSF7, SUGP1, DDX42, DNAJC8, EFTUD2, PRCC, SF3B5, SMNDC1, SNRNP200, WBP11, CDC5L, PPP1R8, PRPF6, BCAS2, NCBP1, PRPF19, PRPF3, SNRPD3, SRSF4, U2AF2, HNRNPUL1, NRIP2, PHF5A, RBM5, RBMX, SNRPA, SRRM2, U2AF1, CCAR1, CFAP20, CIRBP, DDX23, SF3B1, SF3B6, SNRPB2, SNRPE, BUB3, DHX15, PCBP1, PPP1CA, PQBP1, SNRNP70, SRSF1, U2SURP, DDX17, SNRPC, SNRPD2, SNRPF, SNRPG, SRRT, SRSF3, SRSF9, AGGF1, FUS, HNRNPC, HTATSF1, ILF3, PLRG1, SEC31B, TRIR, CWC15, HNRNPAB, PNN, PRPF40A, PRPF8

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 24 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Processing of Capped Intron-Containing Pre-mRNA	5	24.2×	9e-05
mRNA Splicing - Major Pathway	6	19.3×	5e-05
Metabolism of RNA	5	12.3×	1e-03

GO biological processes:

GO term	Partners	Fold	FDR
mRNA splicing, via spliceosome	5	19.9×	1e-03

Disease & clinical

Genetic variants

Variant evidence for PRCC: 83 ClinVar records (0 pathogenic / likely pathogenic); 1 GWAS association.

ClinVar

83 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	58
Likely benign	2
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 36 predictions of 672):

Position(s)	Effect	Δscore	Sites
1:156782280–156782281	acceptor_loss	1.0000	6
1:156782330–156782331	donor_loss	1.0000	4
1:156786587	acceptor_gain	1.0000
1:156791798	donor_gain	1.0000
1:156794663–156794664	acceptor_gain	1.0000	6
1:156794809–156794810	donor_loss	1.0000	3
1:156797274–156797275	acceptor_loss	1.0000	6
1:156797342–156797343	donor_loss	1.0000	5
1:156768240–156768241	donor_loss	0.9900	3
1:156782330	donor_loss	0.9900

AlphaMissense

1,005 missense substitutions predicted likely pathogenic (of 3,159 scored), across 219 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
H455	8	0.999	1.000
F491	8	0.995	1.000
F277	8	0.983	0.997
N473	8	0.977	0.998
H462	8	0.973	1.000
F323	8	0.963	0.998
F394	8	0.952	0.997
N478	8	0.952	0.998
F410	8	0.909	0.997
S440	8	0.878	0.994
D416	8	0.868	0.978
D417	8	0.866	0.967
W475	7	0.999	1.000
E468	7	0.995	0.999
Q456	7	0.994	1.000
E466	7	0.991	0.999
K454	7	0.976	1.000
Q463	7	0.972	1.000
F439	7	0.969	0.996
I457	7	0.964	1.000

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

Cancer	Prognostic	p-value
Liver Hepatocellular Carcinoma (TCGA)	unfavorable	7.9e-05
Kidney Renal Papillary Cell Carcinoma (TCGA)	unfavorable	0.000117

Disease associations

OMIM: gene MIM:179755 | disease phenotypes:

HPO phenotypes

4 phenotypes (HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0001442	Typified by somatic mosaicism
HP:0003829	Typified by incomplete penetrance
HP:0006766	Papillary renal cell carcinoma

GWAS associations

1 associations:

Study	Trait	p-value
GCST004061_1	Sjögren’s syndrome	2e-6

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
methylmercuric chloride	increases expression, affects cotreatment	2
Cadmium Chloride	decreases expression, increases abundance	2
FR900359	affects phosphorylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	increases activity, increases expression, affects binding	1
bisphenol A	affects cotreatment, increases methylation	1
sodium arsenite	decreases expression	1
4-aminophenylarsenoxide	affects binding, decreases reaction	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
nutlin 3	affects cotreatment, increases secretion	1
ICG 001	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic Trioxide	affects binding, decreases reaction	1
Fulvestrant	increases methylation, affects cotreatment	1
Leflunomide	decreases expression	1
Vehicle Emissions	increases abundance, increases expression	1
Cadmium	increases abundance, decreases expression	1
Caffeine	increases phosphorylation	1
Dactinomycin	affects cotreatment, increases secretion	1
Doxorubicin	decreases expression	1
Ketoconazole	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Quercetin	increases phosphorylation	1
Urethane	increases expression	1
Valproic Acid	increases expression	1
Aflatoxin B1	increases methylation	1

Cellosaurus cell lines

6 cell lines: 5 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B099	UOK120	Cancer cell line	Male
CVCL_B105	UOK124	Cancer cell line	Female
CVCL_B123	UOK146	Cancer cell line	Female
CVCL_B3EQ	Abcam HEK293T PRCC KO	Transformed cell line	Female
CVCL_WY83	CL89-12117	Cancer cell line	Male
CVCL_WY84	CL89-17872	Cancer cell line	Male

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.