PSG4

Summary

PSG4 (pregnancy specific beta-1-glycoprotein 4, HGNC:9521) is a protein-coding gene on chromosome 19q13.31, encoding Pregnancy-specific beta-1-glycoprotein 4 (Q00888).

The protein encoded by this gene is a pregnancy-specific glycoprotein (PSG), one of several encoded by a cluster of similar genes on chromosome 19. This gene is a member of the carcinoembryonic antigen (CEA) gene family and may play a role in regulation of the innate immune system. Several transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 5672 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 128 total
• MANE Select transcript: NM_002780

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9521
Approved symbol	PSG4
Name	pregnancy specific beta-1-glycoprotein 4
Location	19q13.31
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000243137
Ensembl biotype	protein_coding
OMIM	176393
Entrez	5672

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 10 protein_coding, 5 retained_intron, 2 nonsense_mediated_decay

ENST00000244295, ENST00000405312, ENST00000433626, ENST00000451895, ENST00000490769, ENST00000495316, ENST00000595949, ENST00000596199, ENST00000596907, ENST00000597349, ENST00000597374, ENST00000597912, ENST00000599371, ENST00000599391, ENST00000599746, ENST00000600572, ENST00000601041

RefSeq mRNA: 4 — MANE Select: NM_002780 NM_001276495, NM_001316339, NM_002780, NM_213633

CCDS: CCDS33039, CCDS46093, CCDS62695

Canonical transcript exons

ENST00000405312 — 6 exons

Exon	Start	End
ENSE00001940408	43192702	43193388
ENSE00003515584	43194995	43195273
ENSE00003682704	43203886	43204251
ENSE00003787511	43194340	43194594
ENSE00003787770	43197997	43198275
ENSE00003850031	43205473	43205638

Expression profiles

Bgee: expression breadth ubiquitous, 123 present calls, max score 95.32.

FANTOM5 (CAGE): breadth broad, TPM avg 5.9860 / max 2307.1170, expressed in 325 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
181245	5.3163	309
181244	0.3100	109
181246	0.0952	59
181239	0.0902	54
181240	0.0642	36
181243	0.0457	15
181242	0.0408	17
181241	0.0237	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
placenta	UBERON:0001987	95.32	gold quality
decidua	UBERON:0002450	81.71	gold quality
type B pancreatic cell	CL:0000169	78.25	gold quality
olfactory bulb	UBERON:0002264	78.08	gold quality
tibialis anterior	UBERON:0001385	77.63	silver quality
buccal mucosa cell	CL:0002336	75.79	silver quality
upper leg skin	UBERON:0004262	75.54	gold quality
upper arm skin	UBERON:0004263	75.38	silver quality
cervix squamous epithelium	UBERON:0006922	75.28	gold quality
pancreatic ductal cell	CL:0002079	73.74	silver quality
lower esophagus mucosa	UBERON:0035834	72.13	gold quality
hair follicle	UBERON:0002073	72.08	gold quality
amniotic fluid	UBERON:0000173	71.32	silver quality
skin of hip	UBERON:0001554	70.10	gold quality
islet of Langerhans	UBERON:0000006	69.30	gold quality
diaphragm	UBERON:0001103	68.50	gold quality
ileal mucosa	UBERON:0000331	68.34	silver quality
quadriceps femoris	UBERON:0001377	67.77	gold quality
vastus lateralis	UBERON:0001379	67.55	gold quality
cervix epithelium	UBERON:0004801	64.34	gold quality
deltoid	UBERON:0001476	63.29	silver quality
triceps brachii	UBERON:0001509	62.89	gold quality
gluteal muscle	UBERON:0002000	62.89	gold quality
skin of leg	UBERON:0001511	61.40	gold quality
zone of skin	UBERON:0000014	61.32	gold quality
tongue squamous epithelium	UBERON:0006919	60.14	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	60.09	gold quality
vena cava	UBERON:0004087	59.89	gold quality
skin of abdomen	UBERON:0001416	59.69	gold quality
germinal epithelium of ovary	UBERON:0001304	58.96	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-7051	yes	285.71
E-ANND-3	no	4.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting PSG4, 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-4694-3P	99.79	69.53	2640
HSA-MIR-377-5P	99.70	65.28	712
HSA-MIR-6086	99.70	65.38	699
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-6727-3P	99.49	65.92	1333
HSA-MIR-143-3P	99.49	69.05	1457
HSA-MIR-4770	99.49	69.09	1451
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-582-5P	99.47	70.79	2635
HSA-MIR-12132	99.47	68.90	1341
HSA-MIR-4284	99.36	65.25	1293
HSA-MIR-4722-3P	99.35	65.22	1099
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-6088	99.29	68.45	1284
HSA-MIR-16-1-3P	98.70	69.23	1538
HSA-MIR-299-5P	98.56	71.14	1140
HSA-MIR-6878-5P	98.49	67.91	2142
HSA-MIR-6827-5P	98.46	64.88	1256
HSA-MIR-3158-3P	98.45	64.25	560
HSA-MIR-124-5P	98.11	67.65	1095
HSA-MIR-4443	98.02	66.25	1928
HSA-MIR-30C-1-3P	97.80	66.36	1499
HSA-MIR-30C-2-3P	97.80	66.45	1499
HSA-MIR-6788-5P	97.80	66.41	1532
HSA-MIR-7855-5P	97.39	67.18	925
HSA-MIR-6869-5P	97.17	67.06	634
HSA-MIR-6515-5P	97.08	65.48	1219
HSA-MIR-6730-3P	97.03	67.54	889
HSA-MIR-7848-3P	95.69	65.00	363

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), PSG3 (ENSG00000221826), PSG7 (ENSG00000221878), PSG1 (ENSG00000231924), PSG2 (ENSG00000242221), PSG11 (ENSG00000243130), CEACAM20 (ENSG00000273777)

Protein

Protein identifiers

Pregnancy-specific beta-1-glycoprotein 4 — Q00888 (reviewed: Q00888)

Alternative names: Pregnancy-specific beta-1-glycoprotein 9

All UniProt accessions (10): Q00888, C9JWP2, M0QY31, M0QYU2, M0R046, M0R0B3, M0R215, M0R2A2, M0R2U8, M0R2Y7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the immunoglobulin superfamily. CEA family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q00888-1	1	yes
Q00888-2	2
Q00888-3	3

RefSeq proteins (4): NP_001263424, NP_001303268, NP_002771, NP_998798 (=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 (29 total): glycosylation site 6, sequence variant 6, sequence conflict 5, domain 4, disulfide bond 3, splice variant 3, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q00888-F1	86.88	0.67

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 (6): 299, 303, 104, 111, 199, 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: 58 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, KOBAYASHI_EGFR_SIGNALING_24HR_UP, XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN, GOZGIT_ESR1_TARGETS_DN, BROWNE_HCMV_INFECTION_48HR_DN, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4, GNF2_KISS1, GOBP_MULTI_MULTICELLULAR_ORGANISM_PROCESS, GNF2_CDKN1C, HENDRICKS_SMARCA4_TARGETS_UP, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL, GNF2_TIMP2, GYORFFY_DOXORUBICIN_RESISTANCE, CHICAS_RB1_TARGETS_CONFLUENT

GO Biological Process (1): 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
multi-organism reproductive process	1
multi-multicellular organism process	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1020 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PSG4	CSH1	P01243	771
PSG4	CSH1	P01243	770
PSG4	PAPPA	Q13219	624
PSG4	ALPP	P05187	452
PSG4	AFP	P02771	447
PSG4	TFPI2	P48307	445
PSG4	SMAD2	Q15796	432
PSG4	PRAMEF14	Q5SWL7	400
PSG4	ZNF574	Q6ZN55	392
PSG4	PSG2	P11465	388
PSG4	A0A096LNM5	A0A096LNM5	386
PSG4	PSG8	Q9UQ74	384
PSG4	PSG1	P11462	382
PSG4	PSG3	Q16557	382
PSG4	SVEP1	Q4LDE5	380

IntAct

12 interactions, top by confidence:

A	B	Type	Score
PSG8	PEX7	psi-mi:“MI:0914”(association)	0.530
GAL3ST1	NDUFA3	psi-mi:“MI:0914”(association)	0.530
PSG3	MGRN1	psi-mi:“MI:0914”(association)	0.530
DSCAM	PSG4	psi-mi:“MI:0915”(physical association)	0.400
PSG4	TNFSF8	psi-mi:“MI:0915”(physical association)	0.400
PSG11	GAPDHS	psi-mi:“MI:0914”(association)	0.350
PSG1	IKBKB	psi-mi:“MI:0914”(association)	0.350
PSG11	ZSWIM8	psi-mi:“MI:0914”(association)	0.350

BioGRID (11): PSG4 (Affinity Capture-MS), PSG4 (Affinity Capture-MS), PSG4 (Two-hybrid), PSG4 (Affinity Capture-MS), PSG4 (Affinity Capture-MS), PSG4 (Affinity Capture-MS), PSG4 (Affinity Capture-MS), PSG4 (Affinity Capture-MS), PSG4 (Affinity Capture-MS), PSG4 (Affinity Capture-MS), PSG4 (Proximity Label-MS)

ESM2 similar proteins: A0A0K2S4Q6, A6NI73, O75019, O75022, O75023, O76036, P0C191, P11464, P11465, P13688, P31997, P40199, P59901, Q00887, Q00888, Q00889, Q08708, Q0V881, Q15238, Q16557, Q28110, Q496F6, Q5M7U7, Q5SQ64, Q6GTX8, Q6ISS4, Q6MG56, Q6PI73, Q863H2, Q863H3, Q8C567, Q8IYS5, Q8MHY9, Q8MJZ2, Q8N149, Q8N423, Q8N6C8, Q8VBT3, Q95JB9, Q96LA5

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, A4FUY1, A6QQC6, A8MVW5, Q14CZ8, Q4VAH7, Q5STE3, Q62845, Q640R3, Q6MZW2, Q8BFR2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	111
Likely benign	10
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

945 predictions. Top by Δscore:

Variant	Effect	Δscore
19:43195269:CTTTG:C	acceptor_gain	0.9800
19:43195274:C:CC	acceptor_gain	0.9800
19:43205593:T:TA	donor_gain	0.9800
19:43193336:C:CT	acceptor_gain	0.9700
19:43193389:C:CC	acceptor_gain	0.9700
19:43203884:A:AC	donor_gain	0.9600
19:43203885:C:CC	donor_gain	0.9600
19:43194473:C:A	donor_gain	0.9500
19:43198276:C:CC	acceptor_gain	0.9500
19:43194472:T:TA	donor_gain	0.9400
19:43197995:A:AC	donor_gain	0.9400
19:43197996:C:CC	donor_gain	0.9400
19:43195271:TTG:T	acceptor_gain	0.9300
19:43204252:C:CC	acceptor_gain	0.9300
19:43205467:CCTCA:C	donor_loss	0.9300
19:43205468:CTCA:C	donor_loss	0.9300
19:43205469:TCA:T	donor_loss	0.9300
19:43205470:CA:C	donor_loss	0.9300
19:43205471:ACCTG:A	donor_loss	0.9300
19:43205472:C:T	donor_loss	0.9300
19:43194591:CCAT:C	acceptor_gain	0.9200
19:43194592:CATC:C	acceptor_gain	0.9200
19:43194599:C:CT	acceptor_gain	0.9200
19:43195276:G:C	acceptor_gain	0.9200
19:43195272:TG:T	acceptor_gain	0.9100
19:43203885:CG:C	donor_gain	0.9100
19:43193386:AGTCT:A	acceptor_loss	0.9000
19:43193387:GTCT:G	acceptor_loss	0.9000
19:43193388:TCTA:T	acceptor_loss	0.9000
19:43193389:CTAC:C	acceptor_loss	0.9000

AlphaMissense

2707 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:43198166:C:A	W180C	0.976
19:43198166:C:G	W180C	0.976
19:43198168:A:G	W180R	0.976
19:43198168:A:T	W180R	0.976
19:43194487:A:G	W366R	0.960
19:43194487:A:T	W366R	0.960
19:43194485:C:A	W366C	0.958
19:43194485:C:G	W366C	0.958
19:43204117:A:G	W67R	0.954
19:43204117:A:T	W67R	0.954
19:43198022:A:C	S228R	0.953
19:43198022:A:T	S228R	0.953
19:43198024:T:G	S228R	0.953
19:43195054:C:G	C310S	0.952
19:43195055:A:T	C310S	0.952
19:43198056:C:G	C217S	0.938
19:43198057:A:T	C217S	0.938
19:43203996:A:G	L107P	0.933
19:43204115:C:A	W67C	0.928
19:43204115:C:G	W67C	0.928
19:43198201:A:G	C169R	0.924
19:43198063:A:C	Y215D	0.923
19:43204000:A:G	S106P	0.923
19:43198200:C:T	C169Y	0.922
19:43198200:C:G	C169S	0.921
19:43198201:A:T	C169S	0.921
19:43198057:A:G	C217R	0.920
19:43195055:A:G	C310R	0.917
19:43198167:C:G	W180S	0.917
19:43195020:A:C	S321R	0.916

dbSNP variants (sampled 300 via entrez): RS1000241267 (19:43198906 C>G,T), RS1000296051 (19:43194770 A>C), RS1000327846 (19:43194895 G>A,C,T), RS1000628923 (19:43194087 T>C), RS1000661475 (19:43194272 A>C), RS1000979273 (19:43197800 G>C), RS1000985551 (19:43202850 TG>T), RS1001018132 (19:43203003 A>G), RS1001134666 (19:43197473 T>G), RS1001322227 (19:43207360 T>C,G), RS1001388827 (19:43207436 A>G), RS1002643060 (19:43192532 A>G), RS1002675312 (19:43203507 C>T), RS1002887476 (19:43205643 C>A,G,T), RS1002986512 (19:43195926 G>A)

Disease associations

OMIM: gene MIM:176393 | 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

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance	3
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	2
bufotalin	increases expression	1
bisphenol A	increases expression	1
ethyl-p-hydroxybenzoate	increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
monomethylarsonous acid	increases expression	1
abrine	increases expression	1
bisphenol S	decreases expression	1
Zoledronic Acid	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Doxorubicin	affects response to substance	1
Estradiol	increases expression	1
Manganese	decreases expression, increases abundance, affects cotreatment	1
Mustard Gas	increases expression	1
Silicon Dioxide	increases expression	1
Valproic Acid	decreases expression	1
8-Bromo Cyclic Adenosine Monophosphate	decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation, increases expression	1
Asbestos, Crocidolite	increases expression	1
Uranium Compounds	increases expression	1
Sodium Selenite	increases expression	1
beta-Naphthoflavone	decreases expression	1
S-Nitrosoglutathione	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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