PRAC2

Summary

PRAC2 (PRAC2 small nuclear protein, HGNC:30143) is a protein-coding gene on chromosome 17q21.32, encoding Protein PRAC2 (D3DTV9).

This gene is highly expressed in prostate, rectum, colon, and testis. This gene may produce a non-coding RNA or may encode a short protein that might localize to the nucleus. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 360205 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001282275

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30143
Approved symbol	PRAC2
Name	PRAC2 small nuclear protein
Location	17q21.32
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000229637
Ensembl biotype	protein_coding
OMIM	610787
Entrez	360205

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 11 protein_coding

ENST00000422730, ENST00000432056, ENST00000936781, ENST00000936782, ENST00000936783, ENST00000936784, ENST00000936785, ENST00000936786, ENST00000936787, ENST00000936788, ENST00000936789

RefSeq mRNA: 2 — MANE Select: NM_001282275 NM_001282275, NM_001282276

CCDS: CCDS74099, CCDS74100

Canonical transcript exons

ENST00000422730 — 2 exons

Exon	Start	End
ENSE00001602878	48724328	48724758
ENSE00001605618	48723185	48723313

Expression profiles

Bgee: expression breadth broad, 32 present calls, max score 92.07.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1726 / max 33.0066, expressed in 52 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
161456	0.1081	37
161455	0.0644	28

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.07	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.92	silver quality
rectum	UBERON:0001052	82.02	gold quality
prostate gland	UBERON:0002367	79.45	gold quality
mucosa of transverse colon	UBERON:0004991	71.63	gold quality
vagina	UBERON:0000996	58.89	gold quality
right testis	UBERON:0004534	58.63	gold quality
left testis	UBERON:0004533	57.77	gold quality
placenta	UBERON:0001987	57.47	gold quality
colonic epithelium	UBERON:0000397	57.36	silver quality
testis	UBERON:0000473	56.77	gold quality
subcutaneous adipose tissue	UBERON:0002190	53.89	gold quality
urinary bladder	UBERON:0001255	53.74	gold quality
muscle layer of sigmoid colon	UBERON:0035805	52.53	gold quality
colon	UBERON:0001155	49.97	gold quality
transverse colon	UBERON:0001157	49.56	gold quality
skin of leg	UBERON:0001511	45.19	gold quality
intestine	UBERON:0000160	42.32	gold quality
adipose tissue	UBERON:0001013	38.61	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ectocervix	UBERON:0012249	35.87	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	35.01	gold quality
zone of skin	UBERON:0000014	34.80	gold quality
uterine cervix	UBERON:0000002	34.54	gold quality
cortex of kidney	UBERON:0001225	32.89	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	19.80
E-ANND-3	no	2.62

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• PRAC2 may have a function in prostate growth and development(PRAC2) (PMID:12746837)
• our study indicated that HOXB13-AS1 could regulate HOXB13 gene expression by methylation HOXB13 promoter and acts as an epigenetic oncogenic in glioma. (PMID:30105866)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Protein PRAC2 — D3DTV9 (reviewed: D3DTV9)

Alternative names: Prostate, rectum and colon expressed gene protein 2

All UniProt accessions (2): A0A087X2F6, D3DTV9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in prostate and testis. Also detected in placenta, muscle, colon, peripheral blood leukocytes and skin.

RefSeq proteins (2): NP_001269204, NP_001269205 (=MANE)

Domains & families (InterPro)

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-D3DTV9-F1	60.27	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 7 (showing top): ZNF407_TARGET_GENES, MED25_TARGET_GENES, GSE37416_CTRL_VS_0H_F_TULARENSIS_LVS_NEUTROPHIL_DN, GSE21927_SPLEEN_VS_BONE_MARROW_MONOCYTE_BALBC_DN, GSE25502_WT_VS_KLF13_KO_THYMIC_MEMORY_LIKE_CD8_TCELL_DN, chr17q21, GSE41867_NAIVE_VS_DAY15_LCMV_CONE13_EFFECTOR_CD8_TCELL_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): nucleus (GO:0005634), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

76 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRAC2	PRAC1	Q96KF2	985
PRAC2	HOXB13	Q92826	916
PRAC2	TDRD10	Q5VZ19	594
PRAC2	TMEM132C	Q8N3T6	526
PRAC2	ANKRD53	Q8N9V6	419
PRAC2	CLXN	Q9HAE3	322
PRAC2	ZNF177	Q13360	300
PRAC2	GXYLT2	A0PJZ3	269
PRAC2	IL22RA1	Q8N6P7	247
PRAC2	RIMBP2	O15034	246
PRAC2	HOXD9	P28356	239
PRAC2	RNF220	Q5VTB9	231
PRAC2	ZNF154	Q13106	225
PRAC2	C17orf107	Q6ZR85	222
PRAC2	HOXB6	P09068	222

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A087WWA1, A0A182BSS5, B1AUF7, D3DTV9, K8DWB5, O12987, O12995, O13557, O30006, O83592, P01073, P03124, P03846, P05679, P08771, P0C5P1, P0C841, P0CV22, P10437, P14311, P16773, P18455, P20218, P23183, P34245, P36283, P38303, P39978, P40519, P53194, P75320, P75602, P81056, P89888, Q04413, Q0UI01, Q28UQ5, Q31CC8, Q3BSH4, Q3E789

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

131 predictions. Top by Δscore:

Variant	Effect	Δscore
17:48723769:G:GT	donor_gain	0.9900
17:48723819:GCC:G	donor_gain	0.9800
17:48724323:CACA:C	acceptor_loss	0.9400
17:48723927:G:GT	donor_gain	0.9200
17:48724512:G:A	acceptor_gain	0.8900
17:48724324:A:AG	acceptor_gain	0.8800
17:48724325:C:G	acceptor_gain	0.8700
17:48724326:A:AG	acceptor_gain	0.8600
17:48724327:G:GG	acceptor_gain	0.8600
17:48724107:GAATG:G	donor_gain	0.8500
17:48724108:AATGG:A	donor_loss	0.8200
17:48724109:ATGGT:A	donor_loss	0.8200
17:48724110:TGGT:T	donor_loss	0.8200
17:48724111:GGT:G	donor_loss	0.8200
17:48724113:T:A	donor_loss	0.8200
17:48724112:G:GG	donor_gain	0.8100
17:48724114:AA:A	donor_loss	0.8100
17:48724324:ACAG:A	acceptor_gain	0.8100
17:48723943:G:GT	donor_gain	0.8000
17:48724476:G:T	acceptor_gain	0.7800
17:48723767:CGGAG:C	donor_loss	0.7700
17:48723768:GGAGG:G	donor_loss	0.7700
17:48723769:GAGG:G	donor_loss	0.7700
17:48723770:AGGTA:A	donor_loss	0.7700
17:48723771:G:C	donor_loss	0.7700
17:48723772:G:GG	donor_loss	0.7700
17:48723773:T:C	donor_loss	0.7700
17:48723816:G:GT	donor_gain	0.7700
17:48723892:A:AG	donor_gain	0.7600
17:48723944:G:T	donor_gain	0.7500

AlphaMissense

573 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:48724678:T:A	W90R	0.900
17:48724678:T:C	W90R	0.900
17:48724504:T:C	F32L	0.895
17:48724506:C:A	F32L	0.895
17:48724506:C:G	F32L	0.895
17:48724680:G:C	W90C	0.847
17:48724680:G:T	W90C	0.847
17:48724554:G:C	W48C	0.767
17:48724554:G:T	W48C	0.767
17:48724499:T:A	L30H	0.746
17:48724462:T:C	F18L	0.740
17:48724464:C:A	F18L	0.740
17:48724464:C:G	F18L	0.740
17:48724679:G:T	W90L	0.733
17:48724552:T:A	W48R	0.721
17:48724552:T:C	W48R	0.721
17:48724679:G:C	W90S	0.721
17:48724494:C:A	N28K	0.720
17:48724494:C:G	N28K	0.720
17:48724502:C:A	A31D	0.695
17:48724496:T:C	L29P	0.690
17:48724517:T:A	L36H	0.686
17:48724535:T:A	I42K	0.682
17:48724496:T:A	L29H	0.679
17:48724513:G:C	G35R	0.676
17:48724535:T:C	I42T	0.673
17:48724507:T:C	F33L	0.654
17:48724509:C:A	F33L	0.654
17:48724509:C:G	F33L	0.654
17:48724505:T:C	F32S	0.650

dbSNP variants (sampled 300 via entrez): RS1000231825 (17:48724469 T>C), RS1000662927 (17:48720065 G>T), RS1000832817 (17:48724735 G>A,C), RS1000965281 (17:48720261 G>A), RS1002156604 (17:48721412 A>G), RS1002619350 (17:48724025 A>T), RS1002688631 (17:48719477 G>A,C), RS1002880445 (17:48719980 C>G,T), RS1003273521 (17:48724421 G>A,C), RS1003537481 (17:48719241 A>ACACACACACACG,ACACACACACG,ACACACACG,ACACACG), RS1003545094 (17:48717350 T>A), RS1003661167 (17:48718624 C>A,T), RS1004376713 (17:48717044 A>G), RS1004405529 (17:48719650 T>C), RS1004681436 (17:48725112 G>A,T)

Disease associations

OMIM: gene MIM:610787 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
entinostat	increases expression	1
Arsenic	increases methylation	1
Benzo(a)pyrene	decreases methylation	1
Drugs, Chinese Herbal	decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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