PSG5

protein-coding

pregnancy specific beta-1-glycoprotein 5, the group of Pregnancy specific glycoproteins|V-set domain containing

Gene summary

The human pregnancy-specific glycoproteins (PSGs) are a group of molecules that are mainly produced by the placental syncytiotrophoblasts during pregnancy. PSGs comprise a subgroup of the carcinoembryonic antigen (CEA) family, which belongs to the immunoglobulin superfamily. For additional general information about the PSG gene family, see PSG1 (MIM 176390).[supplied by OMIM, Oct 2009]

MANE transcript

NM_002781.4

Inheritance

—

ClinVar variants

U:90B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.48

Max pathogenic AF

—

Genomic locus

chr19:43,166,256-43,186,536

External References & Databases

Ensembl (ENSG00000204941)

Transcript & Mutation Effects

hg38 • Region Span ~20.3 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 PSG5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 96

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002781.4. 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
missense			90 clinvar	6 clinvar		96
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	90	7	0	97

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 61 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002781.4	RefSeq	NP_002772.3	5	MANE Select
ENST00000342951.11	Ensembl	ENSP00000344413.6	5	MANE Select
NM_001130014.2	RefSeq	NP_001123486.1	5	Standard
ENST00000366175.7	Ensembl	ENSP00000382334.2	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

Molecular Function

protein binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000366175
Coding exons: 5
Length: 20281
Individuals with no LoFs: 125589
Homozygous LoFs: 0
Heterozygous LoFs: 34
Defined: 125623
p: 0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-3.76	313	173	1.80	0.00000971	2110
Missense (PolyPhen)		103	67.853	1.518		880
Synonymous	-5.27	123	67.8	1.81	0.00000374	684
Loss of Function	-1.91	27	18.2	1.48	0.00000126	196

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0.000098	0.000098	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.951
RVIS EVS: 2.73
RVIS percentile EVS: 98.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.225

Gene Damage Prediction

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