PSG1

protein-coding

pregnancy specific beta-1-glycoprotein 1, the group of V-set domain containing|CD molecules|Pregnancy specific glycoproteins

Gene summary

The human placenta is a multihormonal endocrine organ that produces hormones, enzymes, and other molecules that support fetal survival and development. Pregnancy-specific beta-1-glycoprotein (PSBG, PSG) is a major product of the syncytiotrophoblast, reaching concentrations of 100 to 290 mg/l at term in the serum of pregnant women (Horne et al., 1976 [PubMed 971765]). PSG is a member of the immunoglobulin (Ig) superfamily (Watanabe and Chou, 1988 [PubMed 3257488]; Streydio et al., 1988 [PubMed 3260773]).[supplied by OMIM, Oct 2009]

Previous symbols:

PSBG1

MANE transcript

NM_001184825.2

Inheritance

—

ClinVar variants

U:145B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 2.26

Max pathogenic AF

—

Genomic locus

chr19:42,866,464-42,879,822

External References & Databases

Ensembl (ENSG00000231924)

Transcript & Mutation Effects

hg38 • Region Span ~13.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PSG1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 155

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001184825.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			142 clinvar	9 clinvar		151
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	145	9	0	154

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001184825.2	RefSeq	NP_001171754.1	6	MANE Select
ENST00000436291.7	Ensembl	ENSP00000413041.2	6	MANE Select
NM_001184826.2	RefSeq	NP_001171755.1	6	Standard
NM_001297773.2	RefSeq	NP_001284702.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cell surface interactions at the vascular wall
Hemostasis

Biological Process

female pregnancy
leukocyte migration

Molecular Function

protein binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000244296
Coding exons: 5
Length: 13359
Individuals with no LoFs: 124057
Homozygous LoFs: 98
Heterozygous LoFs: 1505
Defined: 125660
p: 0.00640

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-6.11	495	233	2.13	0.0000135	2716
Missense (PolyPhen)		101	49.353	2.0465		673
Synonymous	-5.73	158	89.2	1.77	0.00000497	854
Loss of Function	-4.46	33	14.6	2.26	8.29e-7	172

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00050	0.00049	rare
Latino/Admixed American	0.0014	0.0014	notable
Ashkenazi Jewish	0.0011	0.0011	notable
East Asian	0.076	0.074	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.0010	0.00096	notable
South Asian	0.0030	0.0027	notable
Other	0.0047	0.0046	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.951
RVIS EVS: 1.85
RVIS percentile EVS: 97.15

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.449

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium