PRRC2B

Summary

PRRC2B (proline rich coiled-coil 2B, HGNC:28121) is a protein-coding gene on chromosome 9q34.13, encoding Protein PRRC2B (Q5JSZ5).

Enables RNA binding activity. Predicted to be involved in cell differentiation. Predicted to act upstream of or within in utero embryonic development.

Source: NCBI Gene 84726 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 445 total
• Druggable target: yes
• MANE Select transcript: NM_013318

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28121
Approved symbol	PRRC2B
Name	proline rich coiled-coil 2B
Location	9q34.13
Locus type	gene with protein product
Status	Approved
Aliases	MGC10526, LQFBS-1
Ensembl gene	ENSG00000288701
Ensembl biotype	protein_coding
OMIM	619544
Entrez	84726

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000682501, ENST00000682525, ENST00000682662, ENST00000683161, ENST00000683353, ENST00000683519, ENST00000684112, ENST00000684596, ENST00000684694, ENST00000684736

RefSeq mRNA: 5 — MANE Select: NM_013318 NM_001384818, NM_001384821, NM_001384822, NM_001384823, NM_013318

CCDS: CCDS48044

Canonical transcript exons

ENST00000683519 — 32 exons

Exon	Start	End
ENSE00003916223	131436620	131436722
ENSE00003916412	131438989	131439061
ENSE00003916697	131482371	131482562
ENSE00003917035	131479252	131479393
ENSE00003917188	131455076	131455166
ENSE00003917278	131487856	131488096
ENSE00003917283	131474454	131476535
ENSE00003917546	131477744	131477949
ENSE00003917639	131491425	131491580
ENSE00003917848	131473508	131473724
ENSE00003917966	131478474	131478619
ENSE00003918012	131447085	131447206
ENSE00003918421	131484948	131485140
ENSE00003918836	131430094	131430259
ENSE00003918993	131483359	131483445
ENSE00003919176	131495740	131500193
ENSE00003919179	131481726	131481808
ENSE00003919221	131486085	131486182
ENSE00003919474	131394086	131394263
ENSE00003919605	131447662	131447804
ENSE00003920481	131467563	131467753
ENSE00003920488	131482710	131482907
ENSE00003920575	131444185	131444328
ENSE00003920609	131464763	131465078
ENSE00003920843	131494405	131494486
ENSE00003921188	131432617	131432794
ENSE00003921393	131446401	131446642
ENSE00003921458	131459164	131459356
ENSE00003921787	131484686	131484790
ENSE00003921827	131492169	131492260
ENSE00003921962	131470788	131470983
ENSE00003922227	131487167	131487294

Expression profiles

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 54.9661 / max 366.6815, expressed in 1824 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
99098	50.0787	1824
99099	1.8805	954
205638	0.8188	482
99096	0.7803	432
99100	0.6518	379
99097	0.3219	141
99101	0.2549	111
99102	0.1793	72

Top tissues by expression

0 total, by Bgee expression score (0-100, higher = more expressed):

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• RNA binding protein PRRC2B mediates translation of specific mRNAs and regulates cell cycle progression. (PMID:37125639)
• Identification and Characterization of a ceRNA Regulatory Network Involving LINC00482 and PRRC2B in Peripheral Blood Mononuclear Cells: Implications for COPD Pathogenesis and Diagnosis. (PMID:38348310)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	PRRC2B	ENSDARG00000079639
mus_musculus	Prrc2b	ENSMUSG00000039262
rattus_norvegicus	Prrc2b	ENSRNOG00000010217
caenorhabditis_elegans		WBGENE00018710

Paralogs (2): PRRC2C (ENSG00000117523), PRRC2A (ENSG00000204469)

Protein

Protein identifiers

Protein PRRC2B — Q5JSZ5 (reviewed: Q5JSZ5)

Alternative names: HLA-B-associated transcript 2-like 1, Proline-rich coiled-coil protein 2B

All UniProt accessions (6): Q5JSZ5, A0A804HIM8, A0A804HJR4, A0A804HKC3, A0A804HKL6, A0A804HKU3

UniProt curated annotations — full annotation on UniProt →

Isoforms (5)

UniProt ID	Names	Canonical?
Q5JSZ5-1	5	yes
Q5JSZ5-2	2
Q5JSZ5-3	3
Q5JSZ5-4	4
Q5JSZ5-5	1

RefSeq proteins (5): NP_001371747, NP_001371750, NP_001371751, NP_001371752, NP_037450* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009738	BAT2_N	Domain
IPR033184	PRRC2	Family

Pfam: PF07001

UniProt features (81 total): compositionally biased region 29, modified residue 21, region of interest 10, sequence conflict 8, splice variant 4, cross-link 3, sequence variant 3, coiled-coil region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JSZ5-F1	38.13	0.02

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 (24): 166, 168, 222, 226, 228, 388, 416, 480, 556, 613, 736, 740, 745, 765, 1132, 1231, 1470, 1507, 1754, 1843 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 143 (showing top): GCM_GSPT1, GCM_BCL2L1, LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN, GCM_NUMA1, LIAO_METASTASIS, GCM_NF2, DOUGLAS_BMI1_TARGETS_UP, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GCM_RBM8A, PARENT_MTOR_SIGNALING_UP, DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP, KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_UP, KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_UP, GCM_RAN, GCM_MLL

GO Biological Process (1): cell differentiation (GO:0030154)

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular developmental process	1
nucleic acid binding	1
binding	1

Protein interactions and networks

STRING

1134 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRRC2B	G3BP2	Q9UN86	623
PRRC2B	WDR91	A4D1P6	444
PRRC2B	UBAP2L	Q14157	443
PRRC2B	ALG3	Q92685	408
PRRC2B	PIERCE2	H3BRN8	400
PRRC2B	SARDH	Q9UL12	399
PRRC2B	LCN10	Q6JVE6	390
PRRC2B	ZNF106	Q9H2Y7	381
PRRC2B	TBC1D22A	Q8WUA7	381
PRRC2B	TERT	O14746	372
PRRC2B	SH3BP5	O60239	368
PRRC2B	FEZ2	Q9UHY8	364
PRRC2B	ZNF770	Q6IQ21	359
PRRC2B	SEC14L5	O43304	355
PRRC2B	CAPRIN1	Q14444	355

IntAct

131 interactions, top by confidence:

A	B	Type	Score
G3BP1	N	psi-mi:“MI:0915”(physical association)	0.980
G3BP2	N	psi-mi:“MI:0915”(physical association)	0.970
EIF3F	EIF3H	psi-mi:“MI:0914”(association)	0.890
EIF3G	EIF3H	psi-mi:“MI:0914”(association)	0.730
ATXN1	PRRC2B	psi-mi:“MI:0915”(physical association)	0.670
EIF3H	EIF3CL	psi-mi:“MI:0914”(association)	0.670
EIF3I	EIF3CL	psi-mi:“MI:0914”(association)	0.640
EIF3F	EIF3CL	psi-mi:“MI:0914”(association)	0.640
EIF3L	EIF3F	psi-mi:“MI:0914”(association)	0.640
EIF3I	EIF3F	psi-mi:“MI:0914”(association)	0.640
Hoxa1	PRRC2B	psi-mi:“MI:0915”(physical association)	0.570
Eif3a	EIF3F	psi-mi:“MI:0915”(physical association)	0.560
rep	SBNO1	psi-mi:“MI:0914”(association)	0.530
CLEC11A	VWA8	psi-mi:“MI:0914”(association)	0.530
JPH4	ZSWIM8	psi-mi:“MI:0914”(association)	0.530
EIF3E	EIF3CL	psi-mi:“MI:0914”(association)	0.530
EIF3L	EIF3CL	psi-mi:“MI:0914”(association)	0.530
NAGK	ZBTB43	psi-mi:“MI:0914”(association)	0.530
PLOD3	COL4A1	psi-mi:“MI:0914”(association)	0.530
PNMA2	CCDC85C	psi-mi:“MI:0914”(association)	0.530

BioGRID (375): KLHL15 (Affinity Capture-MS), ZER1 (Affinity Capture-MS), PRRC2B (Affinity Capture-MS), PRRC2B (Affinity Capture-MS), PRRC2B (Affinity Capture-MS), PRRC2B (Affinity Capture-MS), PRRC2B (Affinity Capture-MS), PRRC2B (Two-hybrid), PRRC2B (Affinity Capture-RNA), PRRC2B (Affinity Capture-Western), PRRC2B (PCA), PRRC2B (Two-hybrid), PRRC2B (Biochemical Activity), PRRC2B (Proximity Label-MS), PRRC2B (Proximity Label-MS)

ESM2 similar proteins: A0A0R4IZ84, A0JMU8, A1L1K8, A5D7H5, B2RRE7, O15234, O60293, O75420, P48634, P61129, P61406, Q04637, Q14444, Q1ECZ4, Q1LZB6, Q3TLH4, Q5CZI8, Q5JSZ5, Q5JVS0, Q5M9G3, Q5RAK6, Q5TM26, Q5U236, Q5VK71, Q5XJD3, Q60865, Q6IMN6, Q6MG48, Q6NZJ6, Q7TPM1, Q7TQG1, Q7TQH0, Q7TSC1, Q80XI3, Q86US8, Q8BWW4, Q8BXJ2, Q8BYK8, Q8K3W3, Q8K3X0

Diamond homologs: P48634, Q3TLH4, Q5JSZ5, Q5TM26, Q6MG48, Q7TPM1, Q7TSC1, Q9SB63, Q9Y520

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 157 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
Formation of the ternary complex, and subsequently, the 43S complex	15	31.7×	8e-17
Ribosomal scanning and start codon recognition	16	29.9×	3e-17
Translation initiation complex formation	15	28.0×	4e-16
SARS-CoV-1 modulates host translation machinery	7	21.2×	2e-06
Eukaryotic Translation Initiation	6	18.2×	4e-05
Cap-dependent Translation Initiation	6	18.2×	4e-05
Formation of a pool of free 40S subunits	15	16.5×	1e-12
Eukaryotic Translation Elongation	6	16.4×	7e-05

GO biological processes:

GO term	Partners	Fold	FDR
formation of cytoplasmic translation initiation complex	11	90.9×	1e-17
translational initiation	11	29.0×	5e-11
regulation of translational initiation	5	17.2×	2e-03
ribosomal small subunit biogenesis	7	11.7×	5e-04
cytoplasmic translation	8	10.9×	2e-04
positive regulation of miRNA transcription	5	10.7×	1e-02

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	361
Likely benign	27
Benign	9

Top pathogenic / likely-pathogenic (0)

SpliceAI

5549 predictions. Top by Δscore:

Variant	Effect	Δscore
9:131432600:T:G	acceptor_gain	1.0000
9:131432615:A:AG	acceptor_gain	1.0000
9:131432615:AGTT:A	acceptor_loss	1.0000
9:131432616:G:A	acceptor_loss	1.0000
9:131432616:G:GA	acceptor_gain	1.0000
9:131432616:GTT:G	acceptor_gain	1.0000
9:131432616:GTTA:G	acceptor_gain	1.0000
9:131436719:GGAG:G	donor_gain	1.0000
9:131436720:GAGG:G	donor_gain	1.0000
9:131436721:AGG:A	donor_loss	1.0000
9:131436722:GGT:G	donor_loss	1.0000
9:131436723:G:GA	donor_loss	1.0000
9:131436724:T:A	donor_loss	1.0000
9:131444327:GA:G	donor_gain	1.0000
9:131444329:G:GG	donor_gain	1.0000
9:131447202:GACGG:G	donor_gain	1.0000
9:131447207:GT:G	donor_loss	1.0000
9:131447208:TGAG:T	donor_loss	1.0000
9:131447660:A:AG	acceptor_gain	1.0000
9:131447661:G:GG	acceptor_gain	1.0000
9:131447661:GAAAA:G	acceptor_gain	1.0000
9:131447802:C:T	donor_gain	1.0000
9:131447802:CAGGT:C	donor_loss	1.0000
9:131447803:AG:A	donor_loss	1.0000
9:131447804:GGTG:G	donor_loss	1.0000
9:131447805:GTG:G	donor_loss	1.0000
9:131455055:T:A	acceptor_gain	1.0000
9:131455056:G:A	acceptor_gain	1.0000
9:131455162:AAGTG:A	donor_gain	1.0000
9:131455164:GTG:G	donor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000023023 (9:131404475 G>A), RS1000094737 (9:131411917 G>C), RS1000129410 (9:131439671 T>A), RS1000156019 (9:131382834 G>A), RS1000184818 (9:131478450 C>G,T), RS1000198759 (9:131371901 C>G,T), RS1000200770 (9:131401334 C>T), RS1000208007 (9:131383133 G>T), RS1000209254 (9:131423713 C>G), RS1000229625 (9:131480517 T>G), RS1000238293 (9:131475140 A>C), RS1000282267 (9:131445267 T>A), RS1000295196 (9:131480217 G>A), RS1000297498 (9:131465291 T>C,G), RS1000332522 (9:131377343 A>C,G)

Disease associations

OMIM: gene MIM:619544 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST008972_20	Urate levels	3.000000e-08
GCST010057_1	Lung function	6.000000e-06
GCST012490_25	Femur bone mineral density x serum urate levels interaction	2.000000e-12
GCST012490_357	Femur bone mineral density x serum urate levels interaction	8.000000e-13

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004531	urate measurement
EFO:0004314	forced expiratory volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6193741 (PROTEIN-PROTEIN INTERACTION)

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
TAK-243	increases sumoylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases methylation	1
arsenite	affects binding, decreases reaction	1
aflatoxin B2	decreases methylation	1
coumarin	increases phosphorylation	1
K 7174	increases expression	1
(+)-JQ1 compound	increases expression	1
mono(carboxy-isooctyl)phthalate	affects expression	1
Resveratrol	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Vorinostat	decreases expression	1
Acetaminophen	increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases mutagenesis	1
Caffeine	affects phosphorylation	1
Cisplatin	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ethyl Methanesulfonate	increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Quercetin	increases expression	1
Ribonucleotides	affects binding	1
Tretinoin	decreases expression	1
Valproic Acid	increases methylation	1
Xylitol	increases 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
CHEMBL4713776	Binding	Protac activity at CRBN/PRRC2B in human BxPC-3 cells assessed as PRRC2B degradation incubated for 16 hrs by proteomic analysis	Discovery of a Napabucasin PROTAC as an Effective Degrader of the E3 Ligase ZFP91. — J Med Chem

Cellosaurus cell lines

2 cell lines: 1 cancer cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_1330	KM-H2	Cancer cell line	Male
CVCL_B3F2	Abcam HEK293T PRRC2B KO	Transformed cell line	Female

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.