PRRC2C

Summary

PRRC2C (proline rich coiled-coil 2C, HGNC:24903) is a protein-coding gene on chromosome 1q24.3, encoding Protein PRRC2C (Q9Y520). Required for efficient formation of stress granules.

Enables RNA binding activity. Involved in stress granule assembly. Located in cytosol.

Source: NCBI Gene 23215 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 19
• Clinical variants (ClinVar): 394 total (top 8% of genes corpus-wide)
• Regional missense constraint (gnomAD): 3 of 11 regions constrained (≈2% of expected missense variation)
• GTEx eGene: eQTL in 20 tissues, sQTL in 4 (q < 0.05)
• Constraint (gnomAD): pLI 1.00 (loss-of-function intolerant), LOEUF 0.29 (highly constrained)
• MANE Select transcript: NM_001387844
• Notable: 394 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24903
Approved symbol	PRRC2C
Name	proline rich coiled-coil 2C
Location	1q24.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1096, XTP2
Ensembl gene	ENSG00000117523
Ensembl biotype	protein_coding
OMIM	617373
Entrez	23215

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 9 protein_coding, 5 protein_coding_CDS_not_defined, 5 nonsense_mediated_decay, 1 retained_intron

MANE Select: ENST00000647382

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 4, TSL 3: 1, TSL 5: 4

ENST00000647382, ENST00000338920, ENST00000367742, ENST00000426496, ENST00000463586, ENST00000467601, ENST00000470689, ENST00000476522, ENST00000480806, ENST00000492811, ENST00000495585, ENST00000498596, ENST00000644916, ENST00000992565, ENST00000992566, ENST00000992567, ENST00001018543, ENST00001105480, ENST00001105482, ENST00001112466

RefSeq mRNA: 2 — MANE Select: NM_001387844 NM_001387844, NM_015172

CCDS: CCDS1296, CCDS91104

Canonical transcript exons

ENST00000647382 — 35 exons

Exon	Start	End
ENSE00000789770	171561018	171561103
ENSE00000789771	171566233	171566421
ENSE00000789772	171566592	171566843
ENSE00000789773	171568247	171568339
ENSE00000789774	171571320	171571421
ENSE00000789775	171574927	171575128
ENSE00000789776	171577434	171577637
ENSE00000789777	171579354	171579466
ENSE00000789778	171579828	171579964
ENSE00000958958	171584419	171584526
ENSE00001151012	171550086	171550240
ENSE00001151016	171545479	171545687
ENSE00001226837	171557240	171558143
ENSE00001372716	171591587	171593511
ENSE00001602651	171539971	171542229
ENSE00001608944	171536029	171536278
ENSE00001682082	171532343	171532961
ENSE00001747804	171535428	171535597
ENSE00001794288	171537263	171537473
ENSE00002342555	171587003	171587221
ENSE00002397175	171583956	171584187
ENSE00003460632	171523435	171523522
ENSE00003484235	171527791	171527844
ENSE00003578430	171515734	171515859
ENSE00003588737	171587648	171587751
ENSE00003600536	171524821	171524965
ENSE00003606342	171512995	171513172
ENSE00003628667	171588379	171588505
ENSE00003645844	171522177	171522259
ENSE00003653650	171514536	171514645
ENSE00003660063	171517591	171517814
ENSE00003664356	171512032	171512200
ENSE00003683382	171523221	171523354
ENSE00003823144	171589369	171589605
ENSE00003922021	171485530	171485735

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 152.3446 / max 7489.8331, expressed in 1828 samples.

Highest expression (Bgee): epithelium of nasopharynx, tendon of biceps brachii, germinal epithelium of ovary, tibia, palpebral conjunctiva.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PRRC2C is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 20 tissues and its splicing (sQTL) in 4 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 24 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Artery Aorta	eqtl	3.6e-23	+0.33	1:171365654:CTGTA:C
Artery Tibial	eqtl	1.9e-21	+0.20	1:171365654:CTGTA:C
Adipose Subcutaneous	eqtl	5.5e-12	+0.27	1:171486183:C:T
Breast Mammary Tissue	eqtl	5.5e-09	-0.18	1:171544336:C:T
Nerve Tibial	eqtl	6.8e-09	+0.26	1:171486183:C:T
Lung	eqtl	2.3e-08	+0.21	1:171486183:C:T
Adipose Visceral Omentum	eqtl	6.7e-08	+0.23	1:171486183:C:T
Thyroid	eqtl	6.5e-06	+0.25	1:171486183:C:T
Nerve Tibial	sqtl	8.4e-06	-1.88	1:170601173:G:T
Testis	sqtl	1.1e-04	-0.67	1:171602498:G:T
Pituitary	eqtl	1.8e-03	-0.29	1:171586740:G:A
Muscle Skeletal	eqtl	2.2e-03	-0.12	1:171651350:C:A
Esophagus Gastroesophageal Junction	eqtl	2.7e-03	+0.47	1:171326841:T:C
Pancreas	eqtl	4.2e-03	+0.16	1:171412396:A:G
Heart Atrial Appendage	eqtl	9.1e-03	-0.13	1:171558378:T:TG
Skin Not Sun Exposed Suprapubic	eqtl	1.8e-02	+0.24	1:171380944:C:T
Whole Blood	eqtl	2.2e-02	-0.06	1:172004774:A:G
Esophagus Mucosa	eqtl	2.5e-02	+0.09	1:171457309:C:A
Cells EBV-transformed lymphocytes	sqtl	3.9e-02	+0.38	1:171553270:T:C
Skin Sun Exposed Lower leg	eqtl	3.9e-02	+0.34	1:171868887:G:A

FANTOM5 promoters

showing 10 of 14 alternative TSS:

Promoter ID	TPM avg	Samples expressed
6609	107.2356	1826
6608	14.9853	1789
6625	7.4331	1429
6626	4.0487	1090
6619	3.7069	1158
6639	3.1797	1224
6640	2.4702	1145
6616	2.0705	1006
6617	1.3971	767
6618	1.3951	701

Top tissues by expression

showing 100 of 295 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
epithelium of nasopharynx	UBERON:0001951	99.61	gold quality
tendon of biceps brachii	UBERON:0008188	99.50	gold quality
germinal epithelium of ovary	UBERON:0001304	99.46	gold quality
tibia	UBERON:0000979	99.35	gold quality
palpebral conjunctiva	UBERON:0001812	99.35	gold quality
visceral pleura	UBERON:0002401	99.34	gold quality
parietal pleura	UBERON:0002400	99.32	gold quality
gingival epithelium	UBERON:0001949	99.24	gold quality
pleura	UBERON:0000977	99.23	gold quality
esophagus squamous epithelium	UBERON:0006920	99.21	gold quality
squamous epithelium	UBERON:0006914	99.15	gold quality
cartilage tissue	UBERON:0002418	99.14	gold quality
Brodmann (1909) area 23	UBERON:0013554	99.08	gold quality
gingiva	UBERON:0001828	98.99	gold quality
cardia of stomach	UBERON:0001162	98.94	gold quality
sural nerve	UBERON:0015488	98.93	gold quality
hair follicle	UBERON:0002073	98.84	gold quality
tongue squamous epithelium	UBERON:0006919	98.74	gold quality
buccal mucosa cell	CL:0002336	98.71	gold quality
pylorus	UBERON:0001166	98.70	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	98.70	gold quality
skin of hip	UBERON:0001554	98.69	gold quality
cervix squamous epithelium	UBERON:0006922	98.65	gold quality
trabecular bone tissue	UBERON:0002483	98.55	gold quality
caput epididymis	UBERON:0004358	98.50	gold quality
mucosa of sigmoid colon	UBERON:0004993	98.49	gold quality
epithelium of esophagus	UBERON:0001976	98.43	gold quality
male germ cell	CL:0000015	98.42	gold quality
sperm	CL:0000019	98.42	gold quality
corpus epididymis	UBERON:0004359	98.42	gold quality
oral cavity	UBERON:0000167	98.40	gold quality
upper leg skin	UBERON:0004262	98.40	gold quality
seminal vesicle	UBERON:0000998	98.39	gold quality
epithelium of mammary gland	UBERON:0003244	98.29	gold quality
penis	UBERON:0000989	98.28	gold quality
mucosa of urinary bladder	UBERON:0001259	98.24	gold quality
choroid plexus epithelium	UBERON:0003911	98.24	gold quality
middle temporal gyrus	UBERON:0002771	98.23	gold quality
mucosa of paranasal sinus	UBERON:0005030	98.22	gold quality
superficial temporal artery	UBERON:0001614	98.21	gold quality
mammary duct	UBERON:0001765	98.20	gold quality
cauda epididymis	UBERON:0004360	98.18	gold quality
oviduct epithelium	UBERON:0004804	98.18	gold quality
medial globus pallidus	UBERON:0002477	98.16	gold quality
globus pallidus	UBERON:0001875	98.13	gold quality
lower lobe of lung	UBERON:0008949	98.11	gold quality
colonic mucosa	UBERON:0000317	98.10	gold quality
mammalian vulva	UBERON:0000997	98.10	gold quality
lateral nuclear group of thalamus	UBERON:0002736	98.10	gold quality
CA1 field of hippocampus	UBERON:0003881	98.09	gold quality
pigmented layer of retina	UBERON:0001782	98.07	gold quality
blood vessel layer	UBERON:0004797	98.07	gold quality
tendon	UBERON:0000043	98.05	gold quality
amniotic fluid	UBERON:0000173	98.03	gold quality
urethra	UBERON:0000057	97.98	gold quality
colonic epithelium	UBERON:0000397	97.98	gold quality
pharyngeal mucosa	UBERON:0000355	97.97	gold quality
lateral globus pallidus	UBERON:0002476	97.94	gold quality
substantia nigra pars reticulata	UBERON:0001966	97.93	gold quality
inferior olivary complex	UBERON:0002127	97.92	gold quality
synovial joint	UBERON:0002217	97.91	gold quality
upper arm skin	UBERON:0004263	97.89	gold quality
bone marrow cell	CL:0002092	97.88	gold quality
jejunal mucosa	UBERON:0000399	97.88	gold quality
superior surface of tongue	UBERON:0007371	97.88	gold quality
thymus	UBERON:0002370	97.84	gold quality
tonsil	UBERON:0002372	97.80	gold quality
epithelial cell of pancreas	CL:0000083	97.79	gold quality
substantia nigra pars compacta	UBERON:0001965	97.78	gold quality
endometrium	UBERON:0001295	97.74	gold quality
medulla oblongata	UBERON:0001896	97.74	gold quality
trigeminal ganglion	UBERON:0001675	97.72	gold quality
mammary gland	UBERON:0001911	97.71	gold quality
thoracic mammary gland	UBERON:0005200	97.69	gold quality
bronchial epithelial cell	CL:0002328	97.66	gold quality
pericardium	UBERON:0002407	97.62	gold quality
jejunum	UBERON:0002115	97.58	gold quality
calcaneal tendon	UBERON:0003701	97.58	gold quality
subthalamic nucleus	UBERON:0001906	97.57	gold quality
superior vestibular nucleus	UBERON:0007227	97.56	gold quality
inferior vagus X ganglion	UBERON:0005363	97.55	gold quality
renal medulla	UBERON:0000362	97.54	gold quality
parotid gland	UBERON:0001831	97.48	gold quality
endothelial cell	CL:0000115	97.47	gold quality
bone marrow	UBERON:0002371	97.47	gold quality
entorhinal cortex	UBERON:0002728	97.47	gold quality
tongue	UBERON:0001723	97.39	gold quality
dorsal root ganglion	UBERON:0000044	97.36	gold quality
nasal cavity epithelium	UBERON:0005384	97.27	gold quality
placenta	UBERON:0001987	97.24	gold quality
parietal lobe	UBERON:0001872	97.23	gold quality
ventral tegmental area	UBERON:0002691	97.23	gold quality
metanephric glomerulus	UBERON:0004736	97.20	gold quality
postcentral gyrus	UBERON:0002581	97.19	gold quality
adult organism	UBERON:0007023	97.19	gold quality
vena cava	UBERON:0004087	97.17	gold quality
bronchus	UBERON:0002185	97.13	gold quality
epithelium of bronchus	UBERON:0002031	97.09	gold quality
pons	UBERON:0000988	97.08	gold quality
gluteal muscle	UBERON:0002000	97.08	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-112	yes	5.38
E-GEOD-130148	yes	4.95
E-MTAB-4850	no	1114.90
E-CURD-135	no	662.24
E-HCAD-4	no	18.92
E-ANND-3	no	0.00

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Cerebral cortex	tissue	86.0	high
Occipital cortex	tissue	86.0
Somatosensory cortex	tissue	84.0
Prefrontal cortex	tissue	82.9
Corpus callosum	tissue	79.5
Hippocampal formation	tissue	79.1
Entorhinal cortex	tissue	79.1
Motor cortex	tissue	78.9
Temporal cortex	tissue	75.9
Thalamus	tissue	74.1
Retrosplenial and cingulate cortex	tissue	73.9
Midbrain	tissue	73.7
Postcentral gyrus	tissue	73.7
Insular cortex	tissue	72.5
Retrosplenial cortex	tissue	71.5
Ventral forebrain	tissue	71.4
Medulla oblongata	tissue	71.2
Cerebellum	tissue	71.2	medium
Substantia nigra	tissue	70.8
Superior colliculi	tissue	70.7
Pons	tissue	70.3
Hypothalamus	tissue	69.7
Putamen	tissue	69.4
Locus coeruleus	tissue	69.2
Spinal cord	tissue	68.9
Olfactory bulb	tissue	68.5
Septum	tissue	66.8
Bone marrow	tissue	66.4	medium
Choroid plexus	tissue	65.6
Nucleus accumbens	tissue	65.2
Hippocampus	tissue	64.4	low
Amygdala	tissue	62.6
Periaqueductal gray	tissue	62.1
Basal ganglia	tissue	61.5	medium
Thymus	tissue	45.3
Lymph node	tissue	41.0	medium
Tonsil	tissue	39.9	medium
Vagina	tissue	38.3	medium
Skin 1	tissue	36.4	medium
Urinary bladder	tissue	35.3	medium
Epididymis	tissue	34.5	medium
Spleen	tissue	32.7	low
Parathyroid gland	tissue	31.3	medium
Placenta	tissue	31.3	high
Appendix	tissue	30.6	medium
Retina	tissue	30.5
Breast	tissue	30.0	medium
Rectum	tissue	29.3	high
Liver	tissue	28.8	medium
Caudate putamen	tissue	27.8
Pituitary gland	tissue	27.4
Testis	tissue	26.7	medium
Stomach 1	tissue	26.7	medium
Frontal cortex	tissue	26.4
Endometrium 1	tissue	26.3	medium
Cervix	tissue	25.0	medium
Seminal vesicle	tissue	24.8	medium
Ovary	tissue	24.6	low
Colon	tissue	24.4	high
Gallbladder	tissue	24.1	high

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Paraventricular nucleus (87.4), Orbitofrontal gyrus, anterior (86.0), White matter (79.5), Vermis (79.3), Flocculonodular lobe (78.3).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting PRRC2C by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 169 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616

Functional genomics

gnomAD constraint: pLI 1, LOEUF 0.287, missense Z 2.48 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000647382 splits into 11 regions with different missense tolerance; 3 are missense-constrained (≈2% of the expected missense variation). Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)	Missense obs / exp	o/e	Constrained
1:171,512,089–171,514,547	71 / 118.9	0.60	no
1:171,514,548–171,522,225	237 / 199.5	1.19	no
1:171,522,226–171,523,489	50 / 88.3	0.57	no
1:171,523,490–171,541,949	1320 / 1395.7	0.95	no
1:171,541,950–171,541,997	4 / 17.9	0.22	yes (p 1.0e-03)
1:171,541,998–171,545,656	178 / 163.0	1.09	no
1:171,545,657–171,550,102	3 / 18.5	0.16	yes (p 3.1e-04)
1:171,550,103–171,571,406	640 / 676.1	0.95	no
1:171,571,407–171,589,570	490 / 663.1	0.74	no
1:171,589,571–171,591,604	3 / 20.9	0.14	yes (p 9.0e-05)
1:171,591,605–171,591,844	78 / 97.7	0.80	no

Literature-anchored findings (GeneRIF, showing 2)

• The KIAA1096 gene is located at 1q23-24 with no overexpression or amplification in normal urothelium, but was significantly upregulated in 30% of tumors. (PMID:12443540)
• 10 genes were down-regulated following treatment of the T-ALL cells with 0.15 and 1.5 microg/mL of metal ores at 72 h (PMID:15747776)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	prrc2c	ENSDARG00000057583
mus_musculus	Prrc2c	ENSMUSG00000040225
rattus_norvegicus	Prrc2c	ENSRNOG00000068743
caenorhabditis_elegans		WBGENE00018710

Paralogs (2): PRRC2A (ENSG00000204469), PRRC2B (ENSG00000288701)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1913754) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 7 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal coat/ hair morphology	1
hyperactivity	1
abnormal vocalization	1
abnormal embryo size	1
abnormal neural tube morphology	1
abnormal neural tube closure	1
preweaning lethality, complete penetrance	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Macaca mulatta	Q5TM26	96.2%	Diamond
Arabidopsis thaliana	Q9SB63	53.8%	Diamond

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
MYOCOS	protein-coding	110806290
MYOC	protein-coding	4653

Protein

Protein identifiers

Protein PRRC2C — Q9Y520 (reviewed: Q9Y520)

Alternative names: BAT2 domain-containing protein 1, HBV X-transactivated gene 2 protein, HBV XAg-transactivated protein 2, HLA-B-associated transcript 2-like 2, Proline-rich and coiled-coil-containing protein 2C

All UniProt accessions (6): A0A2R8Y424, A0A2R8Y7F4, A0A2R8YET2, E7EPN9, H7C5N8, Q9Y520

UniProt curated annotations — full annotation on UniProt →

Function. Required for efficient formation of stress granules.

Subcellular location. Cytoplasm. Stress granule.

Tissue specificity. Overexpressed in bladder cancer.

Isoforms (7)

UniProt ID	Names	Canonical?
Q9Y520-1	1	yes
Q9Y520-2	2
Q9Y520-3	3
Q9Y520-4	4
Q9Y520-5	5
Q9Y520-6	6
Q9Y520-7	7

RefSeq proteins (2): NP_001374773, NP_055987 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009738	BAT2_N	Domain
IPR033184	PRRC2	Family

Pfam: PF07001

UniProt features (127 total): compositionally biased region 46, modified residue 41, region of interest 13, sequence variant 11, splice variant 7, sequence conflict 5, coiled-coil region 2, chain 1, cross-link 1

Structure

Predicted structure (AlphaFold)

No AlphaFold model available for Q9Y520 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol

Antibody reliability (HPA): IH approved · 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 (42)

Type	Positions
Omega-n-methylarginine	2814, 2823, 242, 279, 281
Asymmetric dimethylarginine	2823, 242, 255, 266
Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo2)	1133
N6-acetyllysine	27, 392
Phosphoserine	187, 191, 335, 395, 500, 779, 785, 801, 867, 878, 920, 929, 1242, 1246, 1248, 1249, 1263, 1544, 1983, 2013, 2105, 2143, 2260, 2686, 2694
Phosphothreonine	1265, 1267, 1965, 2673, 2682

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 204 (showing top): E2F_Q4, GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, MORF_SMC1L1, MORF_HDAC1, MORF_UBE2N, YY1_Q6, PATIL_LIVER_CANCER, PUJANA_CHEK2_PCC_NETWORK, MORF_SKP1A, ACCAATC_MIR509, ONKEN_UVEAL_MELANOMA_UP, E2F_Q3, DOANE_RESPONSE_TO_ANDROGEN_DN, YY1_02

GO Biological Process (2): hematopoietic progenitor cell differentiation (GO:0002244), cytoplasmic stress granule assembly (GO:0034063)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (3): cytosol (GO:0005829), cytoplasmic stress granule (GO:0010494), membrane (GO:0016020)

GO top-level categories

8 GO namespaces:

Category	Terms
cellular anatomical structure	2
hemopoiesis	1
cell differentiation	1
membraneless organelle assembly	1
nucleic acid binding	1
binding	1
cytoplasm	1
cytoplasmic ribonucleoprotein granule	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 4 of 7 annotations. The rest are phylogenetic / computational / electronic (IEA).

4 experimentally-supported GO terms:

GO term	NS	Evidence
cytoplasmic stress granule assembly	BP	mutant phenotype
cytosol	CC	direct assay
membrane	CC	high-throughput assay
RNA binding	MF	high-throughput assay

Protein interactions and networks

STRING

showing 15 of 1,578 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRRC2C	UBAP2L	Q14157	716
PRRC2C	CSDE1	O75534	633
PRRC2C	CAPRIN1	Q14444	546
PRRC2C	PLPP6	Q8IY26	467
PRRC2C	ZC3H11A	O75152	448
PRRC2C	CIMIP7	H3BNL1	444
PRRC2C	RSBN1	Q5VWQ0	438
PRRC2C	CLINT1	Q14677	438
PRRC2C	MITD1	Q8WV92	436
PRRC2C	FUBP3	Q96I24	433
PRRC2C	RPRD2	Q5VT52	430
PRRC2C	PIGC	Q92535	427
PRRC2C	PUM1	Q14671	414
PRRC2C	SUCO	Q9UBS9	410
PRRC2C	GOLGA3	Q08378	406

IntAct

Human interaction partners of PRRC2C in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

7 partners by confidence:

Partner	Interaction type	MIscore	Records
H3-4	physical association	0.400	1
HMGN3	physical association	0.400	1
PPFIBP1	physical association	0.400	1
BQRF1	physical association	0.370	1
MDM2	physical association	0.000	1
NR3C1	physical association	0.000	1
PCBD1	physical association	0.000	1

BioGRID (357 interactions; top human partners by supporting records): EIF3A (Cross-Linking-MS (XL-MS); 4 records), CSNK2A2 (Affinity Capture-MS; 3 records), NPM1 (Affinity Capture-MS; 3 records), QPRT (Affinity Capture-MS; 3 records), AURKA (Cross-Linking-MS (XL-MS); 2 records), BAG2 (Affinity Capture-MS; 2 records), CCNF (Affinity Capture-MS; 2 records), CFTR (Affinity Capture-MS; 2 records), CYLD (Affinity Capture-MS; 2 records), FBL (Affinity Capture-MS; 2 records), FMR1 (Proximity Label-MS; 2 records), FXR1 (Proximity Label-MS; 2 records), G3BP1 (Affinity Capture-MS; 2 records), HINFP (Two-hybrid; 2 records), HSP90AA1 (Cross-Linking-MS (XL-MS); 2 records)

Disease & clinical

Genetic variants

Variant evidence for PRRC2C: 394 ClinVar records (0 pathogenic / likely pathogenic); 19 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	311
Likely benign	21
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 27 predictions of 2,368):

Position(s)	Effect	Δscore	Sites
1:171485736–171485737	donor_loss	1.0000	3
1:171512025	acceptor_gain	1.0000
1:171514534	acceptor_gain	1.0000
1:171515721–171515723	acceptor_gain	1.0000	2
1:171515860–171515861	donor_loss	1.0000	5
1:171517577	acceptor_gain	1.0000
1:171517589–171517590	acceptor_loss	1.0000	5
1:171517815–171517816	donor_loss	1.0000	2
1:171522175–171522176	acceptor_loss	1.0000	5
1:171523203	acceptor_gain	1.0000	2

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
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA)	unfavorable	0.000453
Kidney Renal Papillary Cell Carcinoma (TCGA)	unfavorable	0.00071

Disease associations

OMIM: gene MIM:617373 | disease phenotypes:

GWAS associations

19 associations:

Study	Trait	p-value
GCST90002401_350	Platelet distribution width	6e-20
GCST011494_40	Daytime nap	2e-15
GCST007876_91	Estimated glomerular filtration rate	1e-11
GCST010988_253	Adult body size	9e-11
GCST003075_101	Cognitive decline rate in late mild cognitive impairment	2e-10
GCST003075_34	Cognitive decline rate in late mild cognitive impairment	2e-10
GCST005984_3	Glomerular filtration rate	1e-9
GCST008058_174	Estimated glomerular filtration rate	2e-9
GCST010242_472	HDL cholesterol levels	5e-9
GCST005985_3	Creatinine levels	1e-8
GCST006586_46	Urinary albumin excretion	1e-8
GCST008790_4	Urinary albumin-to-creatinine ratio	2e-8
GCST008794_43	Urinary albumin-to-creatinine ratio	2e-8
GCST009640_16	Urinary albumin-to-creatinine ratio	2e-8
GCST001915_1	Alzheimer’s disease (cognitive decline)	9e-7
GCST003075_100	Cognitive decline rate in late mild cognitive impairment	9e-7
GCST003075_26	Cognitive decline rate in late mild cognitive impairment	1e-6
GCST008060_37	Estimated glomerular filtration rate	4e-6
GCST008791_3	Microalbuminuria	6e-6

EFO canonical traits (from GWAS)

6 canonical traits:

EFO ID	Trait name
EFO:0007710	cognitive decline measurement
EFO:0004285	albuminuria
EFO:0007778	urinary albumin to creatinine ratio
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0007828	daytime rest measurement
EFO:0007984	platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067337 (SINGLE PROTEIN)

PharmGKB: 1 entry (CPIC guideline: no)

Binding affinities (BindingDB)

1 measured of 1 human assays (2 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value
CHEMBL5653589	KD	1440 nM

ChEMBL bioactivities

4 potent at pChembl≥5 of 4 total, top 4 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.61	Kd	246	nM	CHEMBL3752910
6.61	ED50	246	nM	CHEMBL3752910
5.60	Kd	2515	nM	CHEMBL5653589
5.60	ED50	2515	nM	CHEMBL5653589

PubChem BioAssay actives

2 with measured affinity, of 4 total; 2 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149097: Binding affinity to human PRRC2C incubated for 45 mins by Kinobead based pull down assay	kd	0.2460	uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149097: Binding affinity to human PRRC2C incubated for 45 mins by Kinobead based pull down assay	kd	2.5152	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Dronabinol	decreases expression, increases expression	4
bisphenol A	decreases expression, increases expression, affects cotreatment	3
Estradiol	decreases expression, increases expression	3
Ozone	affects cotreatment, increases oxidation, increases abundance, increases expression	3
methylmercuric chloride	increases expression	2
trichostatin A	decreases expression, increases expression, affects cotreatment	2
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment, decreases expression	2
Acrolein	affects cotreatment, increases oxidation, increases abundance	2
Air Pollutants	increases oxidation, increases expression, affects cotreatment, increases abundance	2
Benzo(a)pyrene	affects methylation, decreases methylation	2
Tobacco Smoke Pollution	affects expression, increases expression	2
Tretinoin	decreases expression	2
Valproic Acid	affects expression, decreases methylation	2
Aflatoxin B1	decreases methylation, increases methylation	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
TAK-243	affects sumoylation	1
dicrotophos	increases expression	1
geldanamycin	increases expression	1
testosterone enanthate	affects expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
pyrogallol 1,3-dimethyl ether	increases expression, affects cotreatment, affects localization	1
kojic acid	increases expression	1
beta-lapachone	decreases expression	1
sodium arsenite	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652139	Binding	Binding affinity to human PRRC2C incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — *ChemMedChem*

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_F1QW	HyCyte Huh-7 KO-hPRRC2C	Cancer cell line	Male

Clinical trials (associated diseases)

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

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for PRRC2C across ~30M SureChEMBL compounds — explore on Sugi Predict.