PRAC1

Summary

PRAC1 (PRAC1 small nuclear protein, HGNC:30591) is a protein-coding gene on chromosome 17q21.32, encoding Small nuclear protein PRAC1 (Q96KF2). It is a selective cancer dependency (DepMap: 10.8% of cell lines).

This gene is reported to be specifically expressed in prostate, rectum and distal colon. Sequence analysis suggests that it may play a regulatory role in the nucleus.

Source: NCBI Gene 84366 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 9 total
• Cancer dependency (DepMap): dependent in 10.8% of screened cell lines
• MANE Select transcript: NM_032391

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30591
Approved symbol	PRAC1
Name	PRAC1 small nuclear protein
Location	17q21.32
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000159182
Ensembl biotype	protein_coding
OMIM	609819
Entrez	84366

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000290294, ENST00000936891, ENST00000936892, ENST00000936893, ENST00000936894

RefSeq mRNA: 1 — MANE Select: NM_032391 NM_032391

CCDS: CCDS11535

Canonical transcript exons

ENST00000290294 — 2 exons

Exon	Start	End
ENSE00001043845	48721719	48721899
ENSE00001043846	48722318	48722518

Expression profiles

Bgee: expression breadth broad, 71 present calls, max score 98.64.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 2.1631 / max 774.7790, expressed in 53 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
166752	2.1406	51
166753	0.0225	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
rectum	UBERON:0001052	98.64	gold quality
mucosa of sigmoid colon	UBERON:0004993	97.98	gold quality
colonic mucosa	UBERON:0000317	94.11	gold quality
prostate gland	UBERON:0002367	93.78	gold quality
sperm	CL:0000019	88.39	silver quality
mucosa of transverse colon	UBERON:0004991	84.38	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.62	gold quality
vagina	UBERON:0000996	73.31	gold quality
pancreatic ductal cell	CL:0002079	69.99	silver quality
muscle layer of sigmoid colon	UBERON:0035805	66.08	gold quality
urinary bladder	UBERON:0001255	65.52	gold quality
large intestine	UBERON:0000059	63.98	gold quality
colon	UBERON:0001155	62.88	gold quality
tibialis anterior	UBERON:0001385	58.41	silver quality
colonic epithelium	UBERON:0000397	56.45	gold quality
epithelial cell of pancreas	CL:0000083	55.86	gold quality
intestine	UBERON:0000160	54.67	gold quality
transverse colon	UBERON:0001157	54.62	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
ileal mucosa	UBERON:0000331	51.43	silver quality
deltoid	UBERON:0001476	51.11	gold quality
myocardium	UBERON:0002349	50.25	gold quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
ectocervix	UBERON:0012249	47.00	gold quality
quadriceps femoris	UBERON:0001377	46.74	gold quality
uterine cervix	UBERON:0000002	46.23	gold quality
vastus lateralis	UBERON:0001379	45.40	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	1501.91
E-MTAB-8410	yes	919.97
E-ANND-3	yes	12.18

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 10.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

• the pathogenesis of prostate cancer may be due to the expression levels of PRAC protein, and this protein can serve as a potential biomarker for the management of prostate cancer. (PMID:24100630)
• Enhanced methylation of PRAC was positively associated with a high rate of recurrence and progression in nonmuscle invasive bladder cancer patients. (PMID:26074659)
• Discovering the molecular differences between right- and left-sided colon cancer using machine learning methods. (PMID:33076847)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Small nuclear protein PRAC1 — Q96KF2 (reviewed: Q96KF2)

Alternative names: Prostate cancer susceptibility candidate protein 1, Prostate, rectum and colon expressed gene protein

All UniProt accessions (1): Q96KF2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in prostate, rectum, and distal colon, and weakly expressed in bladder. Expressed in prostate cancer cell lines.

RefSeq proteins (1): NP_115767* (*=MANE)

Domains & families (InterPro)

UniProt features (3 total): chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96KF2-F1	59.63	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 15 (showing top): BENPORATH_ES_WITH_H3K27ME3, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, NUYTTEN_EZH2_TARGETS_DN, SCGGAAGY_ELK1_02, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_UP, STK33_SKM_DN, GCNF_01, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_1H_ACT_CD4_TCELL_UP, GSE29614_CTRL_VS_DAY7_TIV_FLU_VACCINE_PBMC_UP, NUYTTEN_NIPP1_TARGETS_UP, TATAAA_TATA_01, BENPORATH_EED_TARGETS, BENPORATH_PRC2_TARGETS, chr17q21, BENPORATH_SUZ12_TARGETS

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (3): nucleoplasm (GO:0005654), cytosol (GO:0005829), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
nuclear lumen	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

168 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRAC1	PRAC2	D3DTV9	985
PRAC1	HOXB13	Q92826	961
PRAC1	ZNF540	Q8NDQ6	449
PRAC1	FAM78A	Q5JUQ0	432
PRAC1	CDC42	P21181	430
PRAC1	NCF2	P19878	424
PRAC1	ZNF671	Q8TAW3	395
PRAC1	ZNF154	Q13106	376
PRAC1	RIMS4	Q9H426	371
PRAC1	ALKAL1	Q6UXT8	370
PRAC1	PCDHAC1	Q9H158	355
PRAC1	ERICH4	A6NGS2	326
PRAC1	KHDRBS2	Q5VWX1	300
PRAC1	GRM6	O15303	300
PRAC1	AKT1	P31749	300

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A023PXM2, A0A8D9PCQ4, B1AK76, G2TRM1, O12159, O13550, O13579, O13583, O14287, P0CX16, P0CX17, P0DPG3, P15972, P17962, P20212, P20464, P21322, P36710, P38322, P38864, P39971, P41659, P68478, P68479, P68537, P68538, P85052, P87282, P92518, Q02781, Q04675, Q0VG73, Q3E7B3, Q3E816, Q54BF4, Q54PP8, Q5VVS0, Q6UDI0, Q6UY13, Q7M6N6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	8
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

259 predictions. Top by Δscore:

Variant	Effect	Δscore
17:48722314:TTAC:T	donor_loss	0.8400
17:48722315:TACCT:T	donor_loss	0.8400
17:48722316:A:AT	donor_loss	0.8400
17:48722317:C:CG	donor_loss	0.8400
17:48722060:AGGT:A	donor_gain	0.8300
17:48722040:C:CA	donor_gain	0.8200
17:48722433:G:A	donor_gain	0.8100
17:48721965:ATG:A	donor_gain	0.8000
17:48722101:C:A	donor_gain	0.7600
17:48722052:C:A	donor_gain	0.7500
17:48722437:G:T	donor_gain	0.7500
17:48722018:A:AC	donor_gain	0.7400
17:48722019:C:CC	donor_gain	0.7400
17:48722063:T:TA	donor_gain	0.7300
17:48722363:T:TA	donor_gain	0.7200
17:48721900:C:CC	acceptor_gain	0.7100
17:48721966:T:C	donor_gain	0.7100
17:48722019:CAG:C	donor_gain	0.7000
17:48721898:TT:T	acceptor_gain	0.6800
17:48722072:T:TA	donor_gain	0.6600
17:48721897:TTTCT:T	acceptor_loss	0.6500
17:48721898:TTCT:T	acceptor_loss	0.6500
17:48721899:TCTAA:T	acceptor_loss	0.6500
17:48721900:CTAAA:C	acceptor_loss	0.6500
17:48721901:T:G	acceptor_loss	0.6500
17:48722050:T:A	donor_gain	0.6400
17:48722194:C:A	donor_gain	0.6400
17:48721896:TTTT:T	acceptor_gain	0.6300
17:48722056:G:A	donor_gain	0.6200
17:48721902:A:C	acceptor_loss	0.6100

AlphaMissense

359 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:48722330:A:C	F21L	0.971
17:48722330:A:T	F21L	0.971
17:48722332:A:G	F21L	0.971
17:48722375:G:C	F6L	0.957
17:48722375:G:T	F6L	0.957
17:48722377:A:G	F6L	0.957
17:48722339:C:A	K18N	0.909
17:48722339:C:G	K18N	0.909
17:48722343:G:A	S17F	0.876
17:48722336:A:C	S19R	0.874
17:48722336:A:T	S19R	0.874
17:48722338:T:G	S19R	0.874
17:48722340:T:A	K18M	0.863
17:48722331:A:C	F21C	0.847
17:48722331:A:G	F21S	0.825
17:48722386:A:G	C3R	0.818
17:48722343:G:T	S17Y	0.811
17:48722376:A:G	F6S	0.811
17:48722376:A:C	F6C	0.806
17:48722370:T:A	D8V	0.800
17:48722384:G:C	C3W	0.800
17:48722318:C:A	K25N	0.789
17:48722318:C:G	K25N	0.789
17:48722349:G:A	T15I	0.785
17:48722385:C:T	C3Y	0.768
17:48721808:A:G	I56T	0.759
17:48722382:G:T	A4D	0.757
17:48722385:C:G	C3S	0.745
17:48722386:A:T	C3S	0.745
17:48722340:T:G	K18T	0.738

dbSNP variants (sampled 300 via entrez): RS1000231825 (17:48724469 T>C), RS1002156604 (17:48721412 A>G), RS1002619350 (17:48724025 A>T), RS1003273521 (17:48724421 G>A,C), RS1005278892 (17:48723783 G>A,C,T), RS1006788167 (17:48723404 T>C), RS1006999866 (17:48723163 C>G), RS1008213567 (17:48723476 G>T), RS1008251113 (17:48723642 T>C), RS1008580009 (17:48722717 CCT>C), RS1010319713 (17:48724369 G>A,C,T), RS1010498767 (17:48724449 C>G,T), RS1011114601 (17:48722036 C>A,G,T), RS1011500336 (17:48723133 G>C), RS1011862509 (17:48723361 A>G)

Disease associations

OMIM: gene MIM:609819 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001942_17	Prostate cancer	2.000000e-09
GCST005042_18	Restless legs syndrome	4.000000e-14
GCST010243_15	Apolipoprotein B levels	1.000000e-13

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004615	apolipoprotein B measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
arsenite	affects binding, increases reaction	1
sodium arsenite	affects methylation	1
entinostat	increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Drugs, Chinese Herbal	decreases expression	1
Aflatoxin B1	decreases methylation	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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