PLAC9

Summary

PLAC9 (placenta associated 9, HGNC:19255) is a protein-coding gene on chromosome 10q22.3, encoding Placenta-specific protein 9 (Q5JTB6).

Predicted to be located in extracellular region.

Source: NCBI Gene 219348 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 26 total
• MANE Select transcript: NM_001012973

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19255
Approved symbol	PLAC9
Name	placenta associated 9
Location	10q22.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000189129
Ensembl biotype	protein_coding
OMIM	612857
Entrez	219348

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000372263, ENST00000372267, ENST00000372270, ENST00000465660, ENST00000941179

RefSeq mRNA: 2 — MANE Select: NM_001012973 NM_001012973, NM_001331125

CCDS: CCDS31232, CCDS86126

Canonical transcript exons

ENST00000372263 — 4 exons

Exon	Start	End
ENSE00001378445	80144223	80144343
ENSE00003994433	80142082	80142179
ENSE00003994434	80144900	80145359
ENSE00003994445	80132730	80132826

Expression profiles

Bgee: expression breadth ubiquitous, 212 present calls, max score 98.42.

FANTOM5 (CAGE): breadth broad, TPM avg 12.9527 / max 330.1672, expressed in 844 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
105843	8.3713	699
105842	4.5244	712
105841	0.0569	17

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
layer of synovial tissue	UBERON:0007616	98.42	gold quality
synovial joint	UBERON:0002217	98.18	gold quality
right coronary artery	UBERON:0001625	97.47	gold quality
left coronary artery	UBERON:0001626	97.31	gold quality
coronary artery	UBERON:0001621	97.15	gold quality
tibial nerve	UBERON:0001323	96.37	gold quality
subcutaneous adipose tissue	UBERON:0002190	96.34	gold quality
apex of heart	UBERON:0002098	96.19	gold quality
right atrium auricular region	UBERON:0006631	96.13	gold quality
adipose tissue	UBERON:0001013	96.12	gold quality
tendon of biceps brachii	UBERON:0008188	96.09	gold quality
endocervix	UBERON:0000458	95.66	gold quality
cardiac atrium	UBERON:0002081	95.53	gold quality
adipose tissue of abdominal region	UBERON:0007808	95.32	gold quality
omental fat pad	UBERON:0010414	95.25	gold quality
peritoneum	UBERON:0002358	95.18	gold quality
skin of hip	UBERON:0001554	94.73	gold quality
ascending aorta	UBERON:0001496	94.64	gold quality
thoracic aorta	UBERON:0001515	94.50	gold quality
upper arm skin	UBERON:0004263	94.37	gold quality
ectocervix	UBERON:0012249	93.97	gold quality
descending thoracic aorta	UBERON:0002345	93.69	gold quality
aorta	UBERON:0000947	93.58	gold quality
pigmented layer of retina	UBERON:0001782	93.50	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	93.31	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.22	gold quality
tibial artery	UBERON:0007610	93.11	gold quality
popliteal artery	UBERON:0002250	93.09	gold quality
left uterine tube	UBERON:0001303	93.00	gold quality
lower esophagus muscularis layer	UBERON:0035833	93.00	gold quality

Single-cell (SCXA)

Detected in 22 experiment(s), a significant marker in 21.

Experiment	Marker?	Max mean expression
E-MTAB-8410	yes	2964.02
E-CURD-112	yes	2831.99
E-MTAB-8322	yes	2399.02
E-HCAD-10	yes	1448.13
E-MTAB-8381	yes	1349.18
E-HCAD-11	yes	1311.58
E-GEOD-134144	yes	1288.62
E-MTAB-6701	yes	1269.27
E-MTAB-7407	yes	1244.38
E-HCAD-38	yes	1115.90
E-HCAD-1	yes	1111.17
E-HCAD-36	yes	1041.51
E-CURD-114	yes	940.00
E-ANND-5	yes	631.42
E-MTAB-10287	yes	58.55

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting PLAC9, 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-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-208A-5P	99.42	70.83	1913
HSA-MIR-208B-5P	99.42	70.83	1952
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-127-5P	97.78	67.64	869

Literature-anchored findings (GeneRIF, showing 1)

• Plac9 is a novel protein that is localized to the cytoplasm and may be secreted through the classic endoplasmic reticulum-Golgi route. The overexpression of Plac9 inhibits cell growth and induces G2/M phase arrest. Conclusion: Our findings reveal a novel role for Plac9 in regulating cell growth. (PMID:30291214)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Plac9	ENSMUSG00000095304
rattus_norvegicus	Plac9	ENSRNOG00000011263

Protein

Protein identifiers

Placenta-specific protein 9 — Q5JTB6 (reviewed: Q5JTB6)

All UniProt accessions (3): Q5JTB4, Q5JTB5, Q5JTB6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the PLAC9 family.

RefSeq proteins (2): NP_001012991, NP_001318054 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027941	PLAC9	Family

Pfam: PF15205

UniProt features (2 total): signal peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JTB6-F1	78.53	0.43

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 87 (showing top): YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, SABATES_COLORECTAL_ADENOMA_DN, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, WNT_UP.V1_UP, SALL4_TARGET_GENES, MIR208B_5P, MIR208A_5P, GSE10463_CD40L_AND_VA347_VS_CD40L_IN_DC_DN, MIR127_5P, GSE13738_RESTING_VS_BYSTANDER_ACTIVATED_CD4_TCELL_UP, MONNIER_POSTRADIATION_TUMOR_ESCAPE_DN, GSE15930_STIM_VS_STIM_AND_TRICHOSTATINA_24H_CD8_T_CELL_UP, GSE15930_STIM_VS_STIM_AND_IL12_72H_CD8_T_CELL_UP, GSE15930_STIM_VS_STIM_AND_IFNAB_72H_CD8_T_CELL_UP, GSE15930_STIM_VS_STIM_AND_TRICHOSTATINA_72H_CD8_T_CELL_UP

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

506 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PLAC9	DUXB	A0A1W2PPF3	608
PLAC9	TMEM254	Q8TBM7	608
PLAC9	C14orf119	Q9NWQ9	525
PLAC9	ANXA11	P50995	472
PLAC9	ARGFX	A6NJG6	460
PLAC9	DUXA	A6NLW8	449
PLAC9	DUX4L2	P0CJ85	441
PLAC9	PYROXD1	Q8WU10	434
PLAC9	DPRX	A6NFQ7	420
PLAC9	JAKMIP3	Q5VZ66	420
PLAC9	ADAT1	Q9BUB4	418
PLAC9	ZNF787	Q6DD87	403
PLAC9	ICA1L	Q8NDH6	401
PLAC9	OR2L13	Q8N349	400
PLAC9	RFLNA	Q6ZTI6	399

IntAct

25 interactions, top by confidence:

A	B	Type	Score
EMILIN1	PLAC9	psi-mi:“MI:0915”(physical association)	0.640
PLAC9	EMILIN1	psi-mi:“MI:0915”(physical association)	0.600
EMILIN1	PLAC9	psi-mi:“MI:0915”(physical association)	0.600
PLAC9	GPRASP2	psi-mi:“MI:0915”(physical association)	0.560
SNAPIN	PLAC9	psi-mi:“MI:0915”(physical association)	0.560
RAPGEF5	PLAC9	psi-mi:“MI:0915”(physical association)	0.370
PLAC9	RNF213	psi-mi:“MI:0915”(physical association)	0.370
PLAC9	CCDC14	psi-mi:“MI:0915”(physical association)	0.370
PLAC9	SSNA1	psi-mi:“MI:0914”(association)	0.350
PLAC9	HSPA5	psi-mi:“MI:0914”(association)	0.350
PLAC9	EMILIN1	psi-mi:“MI:0915”(physical association)	0.000
PLAC9	GPRASP2	psi-mi:“MI:0915”(physical association)	0.000
EMILIN1	PLAC9	psi-mi:“MI:0915”(physical association)	0.000
PLAC9	SNAPIN	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (29): PLAC9 (Two-hybrid), PLAC9 (Two-hybrid), PLAC9 (Two-hybrid), PLAC9 (Two-hybrid), ATP2B4 (Affinity Capture-MS), EMC7 (Affinity Capture-MS), GPD2 (Affinity Capture-MS), ABHD12 (Affinity Capture-MS), EMC4 (Affinity Capture-MS), GDPD1 (Affinity Capture-MS), ZFPL1 (Affinity Capture-MS), TMEM57 (Affinity Capture-MS), RAC3 (Affinity Capture-MS), TENM3 (Affinity Capture-MS), FBXO11 (Affinity Capture-MS)

ESM2 similar proteins: A0A096P2H6, A0A0D9S1R4, A2APA5, A9CBA0, P06740, P06759, P0DKU6, P0DKW1, P0DKW2, P0DKW3, P0DKW4, P0DKY3, P0DML4, P0DML5, P0DML6, P0DMN8, P0DOC4, P0DP53, P0DTG9, P0DTH0, P0DTH1, P0DTH2, P0DTH3, P0DTH4, P0DUP5, P0DUP6, P22749, P33622, P35225, P55056, P55057, P55797, Q0VCT2, Q13790, Q3SYR5, Q3ZRW9, Q5HZE8, Q5JTB6, Q5JX69, Q5JX71

Diamond homologs: Q2TBK3, Q5JTB6, Q8K262

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	22
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

500 predictions. Top by Δscore:

Variant	Effect	Δscore
10:80142177:G:GT	donor_gain	1.0000
10:80144221:AGAT:A	acceptor_gain	1.0000
10:80144222:GATG:G	acceptor_gain	1.0000
10:80132822:GGCCG:G	donor_gain	0.9900
10:80132823:GCCGG:G	donor_gain	0.9900
10:80132825:CGG:C	donor_loss	0.9900
10:80132826:GGT:G	donor_loss	0.9900
10:80132827:G:C	donor_loss	0.9900
10:80132828:T:G	donor_loss	0.9900
10:80142080:A:AG	acceptor_gain	0.9900
10:80142081:G:GG	acceptor_gain	0.9900
10:80142081:GCT:G	acceptor_gain	0.9900
10:80142175:AGGAG:A	donor_loss	0.9900
10:80142176:GGAG:G	donor_gain	0.9900
10:80142176:GGAGG:G	donor_loss	0.9900
10:80142177:GAGG:G	donor_loss	0.9900
10:80142178:AG:A	donor_loss	0.9900
10:80142179:GGTAA:G	donor_loss	0.9900
10:80142180:G:GA	donor_loss	0.9900
10:80142181:T:G	donor_loss	0.9900
10:80144218:TCTA:T	acceptor_loss	0.9900
10:80144219:CTAGA:C	acceptor_loss	0.9900
10:80144220:TA:T	acceptor_loss	0.9900
10:80144221:A:AG	acceptor_gain	0.9900
10:80144222:G:GA	acceptor_gain	0.9900
10:80144222:GAT:G	acceptor_gain	0.9900
10:80144340:GGAG:G	donor_gain	0.9900
10:80144341:G:GT	donor_gain	0.9900
10:80144341:GAG:G	donor_gain	0.9900
10:80144341:GAGGT:G	donor_loss	0.9900

AlphaMissense

608 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:80144269:T:C	L70P	0.923
10:80132790:G:A	G10R	0.888
10:80132790:G:C	G10R	0.888
10:80144248:T:C	L63P	0.859
10:80144236:C:T	T59I	0.854
10:80144248:T:A	L63Q	0.850
10:80144269:T:A	L70Q	0.849
10:80144281:T:C	L74P	0.824
10:80144269:T:G	L70R	0.815
10:80144248:T:G	L63R	0.784
10:80132791:G:A	G10E	0.782
10:80144281:T:G	L74R	0.777
10:80132782:C:A	A7E	0.774
10:80144281:T:A	L74Q	0.771
10:80144245:A:C	H62P	0.760
10:80144290:T:C	L77P	0.756
10:80144258:G:C	E66D	0.750
10:80144258:G:T	E66D	0.750
10:80142163:T:C	L49P	0.744
10:80144235:A:C	T59P	0.744
10:80144260:T:C	V67A	0.733
10:80142176:G:C	E53D	0.710
10:80142176:G:T	E53D	0.710
10:80144239:T:A	V60E	0.709
10:80144272:T:C	L71P	0.702
10:80144278:T:C	L73P	0.696
10:80144292:G:C	A78P	0.692
10:80144236:C:A	T59N	0.690
10:80144260:T:A	V67E	0.669
10:80144235:A:T	T59S	0.660

dbSNP variants (sampled 300 via entrez): RS1000110268 (10:80135267 C>T), RS1000146559 (10:80129677 G>A,T), RS1000524552 (10:80145711 A>G), RS1000813423 (10:80130356 A>C,G,T), RS1000834765 (10:80135086 C>T), RS1001188287 (10:80143220 C>T), RS1001343229 (10:80140462 G>A), RS1001509352 (10:80132605 G>T), RS1001544017 (10:80132870 G>T), RS1001668646 (10:80137580 A>G), RS1001722642 (10:80143538 A>G), RS1001843069 (10:80133901 G>A,C), RS1002063089 (10:80144695 A>AC), RS1002407241 (10:80138940 T>G), RS1002629052 (10:80136427 A>G)

Disease associations

OMIM: gene MIM:612857 | 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
GCST005542_5	Sarcoidosis (non-Lofgren’s syndrome without extrapulmonary manifestations)	4.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, decreases expression	2
aristolochic acid I	increases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Calcitriol	decreases expression	1
Cytarabine	decreases expression	1
Doxorubicin	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Vitallium	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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