PRRC1

Summary

PRRC1 (proline rich coiled-coil 1, HGNC:28164) is a protein-coding gene on chromosome 5q23.2, encoding Protein PRRC1 (Q96M27). May act as a regulator of the protein kinase A (PKA) activity during embryonic development.

Predicted to enable protein kinase A regulatory subunit binding activity. Predicted to be involved in epithelial structure maintenance. Predicted to be located in Golgi apparatus. Predicted to be active in cytoplasm.

Source: NCBI Gene 133619 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 96 total
• MANE Select transcript: NM_130809

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28164
Approved symbol	PRRC1
Name	proline rich coiled-coil 1
Location	5q23.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32875
Ensembl gene	ENSG00000164244
Ensembl biotype	protein_coding
OMIM	621301
Entrez	133619

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 4 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000296666, ENST00000442138, ENST00000507774, ENST00000512635, ENST00000512871, ENST00000513427, ENST00000715263

RefSeq mRNA: 2 — MANE Select: NM_130809 NM_001286808, NM_130809

CCDS: CCDS4143, CCDS68943

Canonical transcript exons

ENST00000296666 — 9 exons

Exon	Start	End
ENSE00001082709	127530294	127530396
ENSE00001082712	127526618	127526778
ENSE00001082713	127523460	127523582
ENSE00001082714	127533623	127533786
ENSE00001082715	127524531	127524920
ENSE00001082716	127547819	127547921
ENSE00001082717	127539040	127539143
ENSE00004026362	127551707	127555085
ENSE00004026363	127517640	127517776

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 97.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 69.8304 / max 404.7280, expressed in 1822 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
58334	52.3734	1817
58335	16.3942	1804
58336	0.6527	367
203676	0.4101	204

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibia	UBERON:0000979	97.27	gold quality
jejunal mucosa	UBERON:0000399	96.23	gold quality
secondary oocyte	CL:0000655	95.39	gold quality
stromal cell of endometrium	CL:0002255	94.96	gold quality
oocyte	CL:0000023	94.84	gold quality
islet of Langerhans	UBERON:0000006	94.82	gold quality
mucosa of sigmoid colon	UBERON:0004993	94.77	gold quality
palpebral conjunctiva	UBERON:0001812	94.64	gold quality
skin of hip	UBERON:0001554	94.51	gold quality
colonic mucosa	UBERON:0000317	94.11	gold quality
mammary duct	UBERON:0001765	93.68	gold quality
endometrium	UBERON:0001295	93.63	gold quality
eye	UBERON:0000970	93.39	gold quality
upper leg skin	UBERON:0004262	93.36	gold quality
corpus epididymis	UBERON:0004359	93.18	gold quality
tendon of biceps brachii	UBERON:0008188	92.99	gold quality
mucosa of paranasal sinus	UBERON:0005030	92.84	gold quality
placenta	UBERON:0001987	92.68	gold quality
germinal epithelium of ovary	UBERON:0001304	92.66	gold quality
epithelium of nasopharynx	UBERON:0001951	92.63	gold quality
nasopharynx	UBERON:0001728	92.62	gold quality
cartilage tissue	UBERON:0002418	92.62	gold quality
cauda epididymis	UBERON:0004360	92.50	gold quality
caput epididymis	UBERON:0004358	92.49	gold quality
adrenal tissue	UBERON:0018303	92.44	gold quality
oral cavity	UBERON:0000167	92.22	gold quality
nipple	UBERON:0002030	92.19	gold quality
penis	UBERON:0000989	92.14	gold quality
amniotic fluid	UBERON:0000173	92.12	gold quality
parietal pleura	UBERON:0002400	91.92	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

197 targeting PRRC1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-1252-5P	100.00	69.80	2774
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-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-340-5P	100.00	72.50	4437

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	prrc1	ENSDARG00000044304
mus_musculus	Prrc1	ENSMUSG00000024594
rattus_norvegicus	Prrc1	ENSRNOG00000016433
caenorhabditis_elegans		WBGENE00015454

Protein

Protein identifiers

Protein PRRC1 — Q96M27 (reviewed: Q96M27)

Alternative names: Proline-rich and coiled-coil-containing protein 1

All UniProt accessions (1): Q96M27

UniProt curated annotations — full annotation on UniProt →

Function. May act as a regulator of the protein kinase A (PKA) activity during embryonic development.

Subunit / interactions. Interacts with PRKAR1A; resulting in PKA activation.

Subcellular location. Golgi apparatus. Cytoplasm.

Tissue specificity. Ubiquitously expressed with higher expression in kidney, liver and placenta. Detected in embryonic kidney cells (HEK293 cells) (at protein level). Specifically expressed in liver.

Miscellaneous. Non-canonical splice sites for exon 9 and exon 10.

Similarity. Belongs to the PRRC1 family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q96M27-1	1	yes
Q96M27-2	2
Q96M27-3	3
Q96M27-4	4
Q96M27-5	5

RefSeq proteins (2): NP_001273737, NP_570721* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026533	NTPase/PRRC1	Domain
IPR026534	PRRC1	Family
IPR029001	ITPase-like_fam	Homologous_superfamily

Pfam: PF01931

UniProt features (15 total): splice variant 6, region of interest 2, sequence conflict 2, compositionally biased region 2, modified residue 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96M27-F1	68.93	0.42

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 (2): 209, 408

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 215 (showing top): RNGTGGGC_UNKNOWN, NKX25_02, MODULE_45, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_UP, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, MODULE_16, OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP, MODULE_239, GATA1_03, GOBP_MULTICELLULAR_ORGANISMAL_LEVEL_HOMEOSTASIS, MORI_PLASMA_CELL_UP, GOBP_EPITHELIAL_STRUCTURE_MAINTENANCE, ACEVEDO_LIVER_CANCER_UP

GO Biological Process (1): epithelial structure maintenance (GO:0010669)

GO Molecular Function (3): protein kinase A regulatory subunit binding (GO:0034237), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (2): cytoplasm (GO:0005737), Golgi apparatus (GO:0005794)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
tissue homeostasis	1
protein kinase A binding	1
protein binding	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

658 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRRC1	SAR1A	Q9NR31	585
PRRC1	MINAR2	P59773	507
PRRC1	DNHD1	Q96M86	454
PRRC1	SPMIP10	Q6ZNM6	418
PRRC1	DNASE1L1	P49184	392
PRRC1	NUDT5	Q9UKK9	384
PRRC1	TEX36	Q5VZQ5	366
PRRC1	CTXN3	Q4LDR2	360
PRRC1	MINAR1	Q9UPX6	348
PRRC1	C5orf63	A6NC05	348
PRRC1	TTC22	Q5TAA0	338
PRRC1	TRAPPC2	P0DI81	328
PRRC1	SEC23A	Q15436	325
PRRC1	TNRC18	O15417	323
PRRC1	FKBP11	Q9NYL4	321

IntAct

52 interactions, top by confidence:

A	B	Type	Score
PLK1	SPAG9	psi-mi:“MI:0914”(association)	0.790
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
SEC23A	SEC24D	psi-mi:“MI:0914”(association)	0.690
HTT	PRRC1	psi-mi:“MI:0915”(physical association)	0.670
YWHAG	BLTP3B	psi-mi:“MI:0914”(association)	0.640
YWHAH	BLTP3B	psi-mi:“MI:0914”(association)	0.570
PRRC1	PIN1	psi-mi:“MI:0915”(physical association)	0.560
PRRC1	SEC23B	psi-mi:“MI:0915”(physical association)	0.560
PIN1	PRRC1	psi-mi:“MI:0915”(physical association)	0.560
SEC23B	PRRC1	psi-mi:“MI:0915”(physical association)	0.560
PRRC1	CDC5	psi-mi:“MI:0915”(physical association)	0.560
CDC5	PRRC1	psi-mi:“MI:0915”(physical association)	0.560
PRRC1		psi-mi:“MI:0915”(physical association)	0.560
	AP3D1	psi-mi:“MI:0914”(association)	0.460
TSG101	PRRC1	psi-mi:“MI:0407”(direct interaction)	0.440
Plk1		psi-mi:“MI:0915”(physical association)	0.400
	PRRC1	psi-mi:“MI:0915”(physical association)	0.370
HTT		psi-mi:“MI:0914”(association)	0.350
apa	NUDT21	psi-mi:“MI:0914”(association)	0.350

BioGRID (74): PRRC1 (Two-hybrid), PRRC1 (Two-hybrid), PRRC1 (Affinity Capture-MS), PRRC1 (Affinity Capture-MS), HNRNPA1 (Co-fractionation), NPEPL1 (Co-fractionation), PAFAH1B2 (Co-fractionation), PPIB (Co-fractionation), PRRC1 (Co-fractionation), PRRC1 (Co-fractionation), PRRC1 (Co-fractionation), PRRC1 (Co-fractionation), PRRC1 (Co-fractionation), PSMG1 (Co-fractionation), RAB1A (Co-fractionation)

ESM2 similar proteins: A0A8M1NHK4, A3KFF6, A6H8J1, O49429, O80678, O80910, P12348, P55265, P94017, P97765, Q08B53, Q13434, Q32SG5, Q3T1I4, Q3TJZ6, Q3UMQ8, Q3UPH1, Q4R3M1, Q5F3N9, Q5FWT1, Q5R679, Q5XJA3, Q5Z8L1, Q66H68, Q6ICG8, Q6P870, Q7G6K7, Q7ZYB4, Q8AVN9, Q8LA32, Q8R478, Q8R4X3, Q93YP4, Q94JZ8, Q969T9, Q96M27, Q9C5P0, Q9C6S1, Q9D529, Q9FF15

Diamond homologs: A6H8J1, Q08B53, Q3T1I4, Q3UPH1, Q5F3I0, Q5XJA3, Q6P870, Q96M27

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	76
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1579 predictions. Top by Δscore:

Variant	Effect	Δscore
5:127523457:T:G	acceptor_gain	1.0000
5:127523458:A:AG	acceptor_gain	1.0000
5:127523459:G:GT	acceptor_gain	1.0000
5:127523459:GT:G	acceptor_gain	1.0000
5:127523556:C:G	donor_gain	1.0000
5:127523579:T:TG	donor_gain	1.0000
5:127523579:TTAGG:T	donor_loss	1.0000
5:127523580:TAGGT:T	donor_loss	1.0000
5:127523581:AGG:A	donor_loss	1.0000
5:127523582:GGT:G	donor_loss	1.0000
5:127523583:GTAC:G	donor_loss	1.0000
5:127523584:T:A	donor_loss	1.0000
5:127530397:G:GG	donor_gain	1.0000
5:127533618:TTTA:T	acceptor_loss	1.0000
5:127533619:TTA:T	acceptor_loss	1.0000
5:127533620:TA:T	acceptor_loss	1.0000
5:127533621:A:AG	acceptor_gain	1.0000
5:127533622:G:GA	acceptor_gain	1.0000
5:127533622:GA:G	acceptor_gain	1.0000
5:127533622:GAA:G	acceptor_gain	1.0000
5:127533622:GAAT:G	acceptor_gain	1.0000
5:127533783:AAAAG:A	donor_loss	1.0000
5:127533784:AAAGT:A	donor_loss	1.0000
5:127533785:AA:A	donor_gain	1.0000
5:127533786:AGT:A	donor_loss	1.0000
5:127533787:G:A	donor_loss	1.0000
5:127533787:GTGA:G	donor_gain	1.0000
5:127533788:T:G	donor_loss	1.0000
5:127533789:G:GT	donor_loss	1.0000
5:127533790:AGT:A	donor_loss	1.0000

AlphaMissense

2831 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:127526774:T:A	I217N	0.999
5:127530361:T:A	I241N	0.999
5:127530361:T:C	I241T	0.999
5:127530361:T:G	I241S	0.999
5:127530370:T:A	L244Q	0.999
5:127530370:T:C	L244P	0.999
5:127530382:T:C	M248T	0.999
5:127533752:C:A	A296D	0.999
5:127539053:G:C	R312P	0.999
5:127551750:G:A	G391D	0.999
5:127551812:T:A	W412R	0.999
5:127551812:T:C	W412R	0.999
5:127530373:A:G	D245G	0.998
5:127530382:T:G	M248R	0.998
5:127547820:T:A	W343R	0.998
5:127547820:T:C	W343R	0.998
5:127551743:T:A	W389R	0.998
5:127551743:T:C	W389R	0.998
5:127551749:G:C	G391R	0.998
5:127526771:T:C	F216S	0.997
5:127526774:T:G	I217S	0.997
5:127533722:T:A	V286D	0.997
5:127533761:C:A	P299Q	0.997
5:127533779:G:A	G305E	0.997
5:127551708:C:A	A377D	0.997
5:127551750:G:T	G391V	0.997
5:127551753:T:C	L392P	0.997
5:127526774:T:C	I217T	0.996
5:127530325:T:A	V229E	0.996
5:127530328:T:A	L230H	0.996

dbSNP variants (sampled 300 via entrez): RS1000133638 (5:127538455 T>C), RS1000140870 (5:127544095 A>G), RS1000223811 (5:127525941 G>C,T), RS1000405185 (5:127545077 C>A), RS1000525760 (5:127554639 C>A,T), RS1000559907 (5:127553092 C>A,T), RS1000629142 (5:127520714 A>C,G), RS1000632073 (5:127553483 T>A,C), RS1000691972 (5:127547364 T>A), RS1000768026 (5:127548760 C>T), RS1000794698 (5:127527382 A>G), RS1000819141 (5:127538801 A>C), RS1000903231 (5:127515955 C>T), RS1001140621 (5:127547001 T>C), RS1001145782 (5:127544861 G>A)

Disease associations

OMIM: gene MIM:621301 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST009391_1080	Metabolite levels	8.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010529	ribose-5-phosphate measurement
EFO:0010530	ribulose-5-phosphate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression, affects cotreatment, increases methylation	4
Dronabinol	increases expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, decreases expression	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
perfluorooctanoic acid	decreases expression	1
zinc chromate	increases abundance, increases expression	1
chromium hexavalent ion	increases abundance, increases expression	1
perfluorooctane sulfonic acid	increases expression	1
pentabromodiphenyl ether	increases expression	1
nutlin 3	affects cotreatment, increases secretion	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
Arsenic Trioxide	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Dactinomycin	affects cotreatment, increases secretion	1
Dexamethasone	decreases expression, affects cotreatment	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Indomethacin	affects cotreatment, decreases expression	1
Ivermectin	decreases expression	1
Dihydrotestosterone	increases expression	1
Thiram	increases expression	1
Tretinoin	decreases expression	1

Clinical trials (associated diseases)

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