PSG4

protein-coding

pregnancy specific beta-1-glycoprotein 4, the group of V-set domain containing|Pregnancy specific glycoproteins

Gene summary

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. [provided by RefSeq, Oct 2015]

MANE transcript

NM_002780.5

Inheritance

—

ClinVar variants

U:113B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.64

Max pathogenic AF

—

Genomic locus

chr19:43,192,702-43,207,299

External References & Databases

Ensembl (ENSG00000243137)

Transcript & Mutation Effects

hg38 • Region Span ~14.6 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 PSG4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 117

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002780.5. 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 clinvar	4
missense			112 clinvar	7 clinvar	1 clinvar	120
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	113	8	3	124

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002780.5	RefSeq	NP_002771.2	6	MANE Select
ENST00000405312.8	Ensembl	ENSP00000384770.3	6	MANE Select
NM_001276495.2	RefSeq	NP_001263424.1	5	Standard
NM_001316339.2	RefSeq	NP_001303268.1	5	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

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000405312
Coding exons: 6
Length: 14598
Individuals with no LoFs: 125658
Homozygous LoFs: 2
Heterozygous LoFs: 24
Defined: 125684
p: 0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-4.21	403	225	1.79	0.0000124	2669
Missense (PolyPhen)		134	81.961	1.6349		1042
Synonymous	-6.23	158	84.9	1.86	0.00000442	835
Loss of Function	-2.74	35	21.3	1.64	0.00000137	226

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000060	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00013	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00014	rare
South Asian	0.00020	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.960
RVIS EVS: 2.18
RVIS percentile EVS: 98.08

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.239

Gene Damage Prediction

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