PSG3

protein-coding

pregnancy specific beta-1-glycoprotein 3, the group of Pregnancy specific glycoproteins|V-set domain containing

Gene summary

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).[supplied by OMIM, Oct 2009]

MANE transcript

NM_021016.4

Inheritance

—

ClinVar variants

U:127B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.41

Max pathogenic AF

—

Genomic locus

chr19:42,721,638-42,740,481

External References & Databases

Ensembl (ENSG00000221826)

Transcript & Mutation Effects

hg38 • Region Span ~18.8 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 PSG3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 136

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021016.4. 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			1 clinvar	1 clinvar		2
missense			125 clinvar	13 clinvar		138
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	127	14	0	141

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021016.4	RefSeq	NP_066296.2	6	MANE Select
ENST00000327495.10	Ensembl	ENSP00000332215.5	6	MANE Select
ENST00000594378.1	Ensembl	ENSP00000469292.1	2	Standard
ENST00000595140.5	Ensembl	ENSP00000468936.1	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

defense response
female pregnancy

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000327495
Coding exons: 6
Length: 18932
Individuals with no LoFs: 125699
Homozygous LoFs: 0
Heterozygous LoFs: 48
Defined: 125747
p: 0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-5.18	444	225	1.97	0.0000129	2735
Missense (PolyPhen)		125	69.189	1.8067		965
Synonymous	-6.78	170	88.7	1.92	0.00000516	853
Loss of Function	-1.81	32	22.7	1.41	0.00000156	245

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00040	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000096	0.000046	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00023	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.967
RVIS EVS: 1.18
RVIS percentile EVS: 92.83

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0514

Gene Damage Prediction

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