PSG9
protein-codingpregnancy specific beta-1-glycoprotein 9, the group of V-set domain containing|Pregnancy specific glycoproteins
Gene summary
The protein encoded by this gene is a member of the pregnancy-specific glycoprotein (PSG) family. This protein family and the closely related carcinoembryonic antigen cell adhesion molecule (CEACAM) gene family are both members of the immunoglobulin superfamily, and are organized as a large gene cluster. This protein is thought to inhibit platelet-fibrinogen interactions. Several studies suggest that reduced serum concentrations of PSGs are associated with fetal growth restrictions, while up-regulation of this gene has been observed in colorectal cancers. Several pseudogenes of this gene are found on chromosome 19. Alternative splicing results in multiple transcript variants that encode multiple protein isoforms. [provided by RefSeq, Sep 2014]
- PSG11
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~57.7 kbGenCC 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 PSG9 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002784.5. 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 | 2 | 1 | 3 | |||
| missense | 135 | 9 | 1 | 145 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 137 | 10 | 1 | 148 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002775.3 | 6 | MANE Select | |
| Ensembl | ENSP00000270077.3 | 6 | MANE Select | |
| RefSeq | NP_001288636.1 | 5 | Standard | |
| RefSeq | NP_001288637.1 | 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:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000270077
- Coding exons
- 6
- Length
- 57740
- Individuals with no LoFs
- 101009
- Homozygous LoFs
- 2422
- Heterozygous LoFs
- 22316
- Defined
- 125747
- p
- 0.104
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -2.92 | 359 | 234 | 1.54 | 0.0000131 | 2731 |
| Missense (PolyPhen) | 77 | 65.773 | 1.1707 | 905 | ||
| Synonymous | -5.43 | 156 | 90.3 | 1.73 | 0.00000517 | 841 |
| Loss of Function | -1.67 | 28 | 20.0 | 1.40 | 0.00000119 | 226 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.20 | 0.20 | notable |
| Latino/Admixed American | 0.14 | 0.14 | notable |
| Ashkenazi Jewish | 0.081 | 0.067 | notable |
| East Asian | 0.37 | 0.36 | notable |
| Finnish | 0.090 | 0.083 | notable |
| European (Non-Finnish) | 0.064 | 0.060 | notable |
| South Asian | 0.099 | 0.085 | notable |
| Other | 0.10 | 0.093 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.962
- RVIS EVS
- 1.61
- RVIS percentile EVS
- 95.92
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.566
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |