PSG3

Summary

PSG3 (pregnancy specific beta-1-glycoprotein 3, HGNC:9520) is a protein-coding gene on chromosome 19q13.2, encoding Pregnancy-specific beta-1-glycoprotein 3 (Q16557).

The human pregnancy-specific glycoproteins (PSGs) are a family of proteins that are synthesized in large amounts by placental trophoblasts and released into the maternal circulation during pregnancy. Molecular cloning and analysis of several PSG genes has indicated that the PSGs form a subgroup of the carcinoembryonic antigen (CEA) gene family, which belongs to the immunoglobulin superfamily of genes. Members of the CEA family consist of a single N domain, with structural similarity to the immunoglobulin variable domains, followed by a variable number of immunoglobulin constant-like A and/or B domains. Most PSGs have an arg-gly-asp (RGD) motif, which has been shown to function as an adhesion recognition signal for several integrins, in the N-terminal domain (summary by Teglund et al., 1994 [PubMed 7851896]). For additional general information about the PSG gene family, see PSG1 (MIM 176390).

Source: NCBI Gene 5671 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 142 total
• MANE Select transcript: NM_021016

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9520
Approved symbol	PSG3
Name	pregnancy specific beta-1-glycoprotein 3
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000221826
Ensembl biotype	protein_coding
OMIM	176392
Entrez	5671

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000327495, ENST00000490592, ENST00000594378, ENST00000595140, ENST00000597009, ENST00000614582

RefSeq mRNA: 1 — MANE Select: NM_021016 NM_021016

CCDS: CCDS12611

Canonical transcript exons

ENST00000327495 — 7 exons

Exon	Start	End
ENSE00001510270	42721642	42722090
ENSE00001820313	42740321	42740481
ENSE00002454599	42729123	42729377
ENSE00003496422	42723942	42724025
ENSE00003532258	42729778	42730056
ENSE00003603974	42732784	42733062
ENSE00003655753	42738724	42739089

Expression profiles

Bgee: expression breadth broad, 94 present calls, max score 97.04.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 6.4321 / max 6055.2012, expressed in 36 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
181210	6.4321	36

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
placenta	UBERON:0001987	97.04	gold quality
decidua	UBERON:0002450	91.24	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.25	silver quality
oral cavity	UBERON:0000167	77.18	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	72.91	gold quality
tibialis anterior	UBERON:0001385	69.61	silver quality
adrenal tissue	UBERON:0018303	68.40	gold quality
nasal cavity epithelium	UBERON:0005384	67.06	gold quality
oocyte	CL:0000023	65.29	gold quality
gingiva	UBERON:0001828	65.18	gold quality
gingival epithelium	UBERON:0001949	64.87	gold quality
rectum	UBERON:0001052	64.11	gold quality
buccal mucosa cell	CL:0002336	63.03	gold quality
ileal mucosa	UBERON:0000331	62.35	gold quality
amniotic fluid	UBERON:0000173	61.86	gold quality
cervix epithelium	UBERON:0004801	61.71	gold quality
cardiac muscle of right atrium	UBERON:0003379	61.47	gold quality
endometrium epithelium	UBERON:0004811	60.93	gold quality
left ventricle myocardium	UBERON:0006566	60.62	gold quality
mucosa of urinary bladder	UBERON:0001259	59.57	gold quality
pharyngeal mucosa	UBERON:0000355	59.12	gold quality
trachea	UBERON:0003126	58.88	gold quality
parotid gland	UBERON:0001831	58.82	gold quality
body of tongue	UBERON:0011876	58.71	gold quality
pancreatic ductal cell	CL:0002079	58.66	silver quality
diaphragm	UBERON:0001103	58.30	gold quality
heart right ventricle	UBERON:0002080	58.25	gold quality
lower esophagus mucosa	UBERON:0035834	58.04	gold quality
superior surface of tongue	UBERON:0007371	57.93	gold quality
tongue	UBERON:0001723	57.79	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.42

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): KLF6

miRNA regulators (miRDB)

43 targeting PSG3, 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-4262	100.00	73.26	3931
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-2052	99.79	69.37	2031
HSA-MIR-556-3P	99.74	68.75	1203
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-519A-3P	99.67	71.67	1868
HSA-MIR-519B-3P	99.67	71.67	1868
HSA-MIR-519C-3P	99.67	71.67	1870
HSA-MIR-516B-5P	99.56	66.33	1495
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-6839-3P	99.39	68.86	1301

Cross-species orthologs

0 orthologs

Paralogs (24): CEACAM21 (ENSG00000007129), CEACAM7 (ENSG00000007306), CEACAM1 (ENSG00000079385), CEACAM6 (ENSG00000086548), CEACAM4 (ENSG00000105352), CEACAM5 (ENSG00000105388), PSG8 (ENSG00000124467), CEACAM8 (ENSG00000124469), HEPACAM (ENSG00000165478), PSG6 (ENSG00000170848), CEACAM3 (ENSG00000170956), PSG9 (ENSG00000183668), CEACAM19 (ENSG00000186567), HEPACAM2 (ENSG00000188175), PSG5 (ENSG00000204941), CEACAM18 (ENSG00000213822), CEACAM16 (ENSG00000213892), VSTM5 (ENSG00000214376), PSG7 (ENSG00000221878), PSG1 (ENSG00000231924), PSG2 (ENSG00000242221), PSG11 (ENSG00000243130), PSG4 (ENSG00000243137), CEACAM20 (ENSG00000273777)

Protein

Protein identifiers

Pregnancy-specific beta-1-glycoprotein 3 — Q16557 (reviewed: Q16557)

Alternative names: Carcinoembryonic antigen SG5

All UniProt accessions (3): Q16557, M0QX68, M0QXP2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the immunoglobulin superfamily. CEA family.

RefSeq proteins (1): NP_066296* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR013106	Ig_V-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR050831	CEA_cell_adhesion	Family

Pfam: PF07686, PF13895, PF13927

UniProt features (22 total): sequence variant 6, glycosylation site 4, domain 4, disulfide bond 3, sequence conflict 2, signal peptide 1, chain 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q16557-F1	85.48	0.61

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (3): 169–217, 262–310, 354–394

Glycosylation sites (4): 303, 104, 111, 268

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-202733	Cell surface interactions at the vascular wall

MSigDB gene sets: 57 (showing top): KOBAYASHI_EGFR_SIGNALING_24HR_UP, BROWNE_HCMV_INFECTION_6HR_DN, GOZGIT_ESR1_TARGETS_DN, MODULE_478, BROWNE_HCMV_INFECTION_48HR_DN, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4, BLALOCK_ALZHEIMERS_DISEASE_UP, GNF2_KISS1, GOBP_MULTI_MULTICELLULAR_ORGANISM_PROCESS, GNF2_CDKN1C, REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL, GNF2_TIMP2, PEDRIOLI_MIR31_TARGETS_DN, CYCLIN_D1_KE_.V1_DN, MIR607

GO Biological Process (2): defense response (GO:0006952), female pregnancy (GO:0007565)

GO Molecular Function (0):

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

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Hemostasis	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
response to stress	1
multi-organism reproductive process	1
multi-multicellular organism process	1
cellular anatomical structure	1

Protein interactions and networks

STRING

900 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PSG3	CSH1	P01243	785
PSG3	CSH1	P01243	781
PSG3	PAPPA	Q13219	666
PSG3	SPANXN3	Q5MJ09	598
PSG3	AFP	P02771	479
PSG3	TFPI2	P48307	475
PSG3	ALPP	P05187	469
PSG3	ADH4	P08319	426
PSG3	LGALS1	P09382	404
PSG3	PSG9	Q00887	383
PSG3	PSG4	Q00888	382
PSG3	A0A096LNM5	A0A096LNM5	368
PSG3	ARID1A	O14497	366
PSG3	PAPPA2	Q9BXP8	358
PSG3	CGB5	P01233	349

IntAct

16 interactions, top by confidence:

A	B	Type	Score
GAL3ST1	NDUFA3	psi-mi:“MI:0914”(association)	0.530
PSG3	MGRN1	psi-mi:“MI:0914”(association)	0.530
PSG8	MGRN1	psi-mi:“MI:0914”(association)	0.530
PSG3	NLGN3	psi-mi:“MI:0915”(physical association)	0.370
PSG3	TENT5A	psi-mi:“MI:0915”(physical association)	0.370
PSG3	SKIL	psi-mi:“MI:0915”(physical association)	0.370
PSG3	PRKD2	psi-mi:“MI:0915”(physical association)	0.370
PSG3	ATF7IP	psi-mi:“MI:0915”(physical association)	0.370
TMPRSS11A	PAK4	psi-mi:“MI:0914”(association)	0.350
PSG3	PSG1	psi-mi:“MI:0914”(association)	0.350
TADA3	CYTH3	psi-mi:“MI:0914”(association)	0.350

BioGRID (29): MEGF8 (Affinity Capture-MS), PSG9 (Affinity Capture-MS), PSG1 (Affinity Capture-MS), FBLN1 (Affinity Capture-MS), ANKRD46 (Affinity Capture-MS), PSG3 (Affinity Capture-MS), PSG3 (Two-hybrid), PSG1 (Affinity Capture-MS), PSG9 (Affinity Capture-MS), PSG3 (Affinity Capture-MS), ANKRD46 (Affinity Capture-MS), PSG9 (Affinity Capture-MS), INPP5A (Affinity Capture-MS), ANKRD46 (Affinity Capture-MS), PSG3 (Affinity Capture-MS)

ESM2 similar proteins: A1A5C7, A5D7H1, A6H7A0, A6NJW4, A6QLN9, A8MUP2, A8MXK1, B0BMW8, B0BNL6, O35393, O62657, O75078, P52875, P55244, P56880, P57791, Q08334, Q0V881, Q15768, Q16557, Q2M1K6, Q3SZQ2, Q3UHH2, Q4V899, Q5E9H2, Q5FYB0, Q5M7U7, Q5R6I6, Q5RCI5, Q5SQ64, Q642A6, Q6PCB0, Q7TPB4, Q8BM89, Q8BZH0, Q8N431, Q8N5I2, Q8R2R5, Q8R2Z5, Q8VE98

Diamond homologs: A0A0B4J1L0, D3ZQE1, E9QA28, O75871, P06731, P11464, P11465, P13688, P16573, P31809, P31997, P40198, P40199, Q00887, Q00888, Q00889, Q13046, Q14002, Q15238, Q16557, Q2WEN9, Q3KPI0, Q3UKK2, Q61400, Q63111, Q810J1, Q925P2, Q9D2Z1, Q9UQ72, Q9UQ74, A0A140LHF2, P0DP72, P35329, Q15223, Q15746, Q58EX2, Q6V4S5, Q96FE5, Q9D1T0, Q9GL76

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	123
Likely benign	14
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

987 predictions. Top by Δscore:

Variant	Effect	Δscore
19:42724026:C:CC	acceptor_gain	0.9900
19:42724030:CA:C	acceptor_gain	0.9900
19:42724031:A:AC	acceptor_gain	0.9900
19:42724031:A:C	acceptor_gain	0.9900
19:42729256:C:A	donor_gain	0.9900
19:42733063:C:CC	acceptor_gain	0.9900
19:42722087:CTGT:C	acceptor_gain	0.9800
19:42738722:A:AC	donor_gain	0.9800
19:42738723:C:CC	donor_gain	0.9800
19:42740441:T:TA	donor_gain	0.9800
19:42730057:C:CC	acceptor_gain	0.9700
19:42730059:G:C	acceptor_gain	0.9700
19:42740315:CCTCA:C	donor_loss	0.9700
19:42740316:CTCA:C	donor_loss	0.9700
19:42740317:TCAC:T	donor_loss	0.9700
19:42740318:CACC:C	donor_loss	0.9700
19:42740320:C:A	donor_loss	0.9700
19:42723952:T:TA	donor_gain	0.9600
19:42724023:GAG:G	acceptor_gain	0.9600
19:42724024:AGCTG:A	acceptor_loss	0.9600
19:42724025:GCTG:G	acceptor_loss	0.9600
19:42724026:C:CG	acceptor_loss	0.9600
19:42724027:T:G	acceptor_loss	0.9600
19:42729255:T:TA	donor_gain	0.9600
19:42730055:CG:C	acceptor_gain	0.9600
19:42730055:CGCTG:C	acceptor_gain	0.9600
19:42732782:A:AC	donor_gain	0.9600
19:42732783:C:CC	donor_gain	0.9600
19:42733058:CTCCA:C	acceptor_gain	0.9600
19:42733061:CA:C	acceptor_gain	0.9600

AlphaMissense

2768 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:42729837:C:G	C310S	0.963
19:42729838:A:T	C310S	0.963
19:42729268:C:A	W366C	0.955
19:42729268:C:G	W366C	0.955
19:42738955:A:G	W67R	0.954
19:42738955:A:T	W67R	0.954
19:42729270:A:G	W366R	0.953
19:42729270:A:T	W366R	0.953
19:42732809:A:C	S228R	0.951
19:42732809:A:T	S228R	0.951
19:42732811:T:G	S228R	0.951
19:42732843:C:G	C217S	0.949
19:42732844:A:T	C217S	0.949
19:42732953:C:A	W180C	0.940
19:42732953:C:G	W180C	0.940
19:42732955:A:G	W180R	0.939
19:42732955:A:T	W180R	0.939
19:42732987:C:G	C169S	0.937
19:42732988:A:T	C169S	0.937
19:42732988:A:G	C169R	0.932
19:42738834:A:G	L107P	0.932
19:42738953:C:A	W67C	0.931
19:42738953:C:G	W67C	0.931
19:42732987:C:T	C169Y	0.926
19:42729185:C:G	C394S	0.924
19:42729186:A:T	C394S	0.924
19:42729838:A:G	C310R	0.923
19:42732844:A:G	C217R	0.919
19:42732850:A:C	Y215D	0.912
19:42729306:A:G	C354R	0.911

dbSNP variants (sampled 300 via entrez): RS1000146576 (19:42724366 T>A), RS1000197508 (19:42729654 C>T), RS1000239652 (19:42731196 T>C), RS1000274689 (19:42741825 C>A,G,T), RS1000360599 (19:42734135 G>T), RS1000391721 (19:42734249 T>C), RS1000518491 (19:42724206 T>A), RS1000590048 (19:42727024 T>C), RS1000736390 (19:42733583 C>T), RS1000802882 (19:42730352 C>A,T), RS1000862189 (19:42731038 A>G), RS1000979239 (19:42730503 A>G), RS1001039207 (19:42739502 C>T), RS1001171128 (19:42742181 G>A), RS1001297719 (19:42724719 A>G)

Disease associations

OMIM: gene MIM:176392 | 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

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

Chemical	Actions (top 5)	PubMed papers
potassium chromate(VI)	affects cotreatment, decreases expression, increases expression	2
Smoke	decreases reaction, decreases expression	2
afuresertib	increases expression	1
testosterone undecanoate	affects cotreatment, increases expression	1
sodium arsenite	decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
chromium hexavalent ion	affects expression	1
2-palmitoylglycerol	increases expression	1
abrine	increases expression	1
Decitabine	decreases expression, decreases reaction	1
Benzo(a)pyrene	increases methylation	1
Cadmium	affects expression	1
Chromium	increases expression	1
Silicon Dioxide	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Aflatoxin B1	decreases methylation	1
Levonorgestrel	increases expression, affects cotreatment	1
Asbestos, Crocidolite	increases expression	1
beta-Naphthoflavone	decreases expression	1

Clinical trials (associated diseases)

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