PSD2
protein-codingpleckstrin and Sec7 domain containing 2, the group of Pleckstrin homology domain containing|Pleckstrin and Sec7 domain containing
Gene summary
Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in vesicle-mediated transport. Predicted to be located in cleavage furrow. Predicted to be active in ruffle membrane. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~48.7 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 PSD2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032289.4. 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 | 2 | 1 | 1 | 4 | ||
| missense | 124 | 3 | 2 | 129 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 126 | 4 | 3 | 133 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_115665.1 | 14 | MANE Select | |
| Ensembl | ENSP00000274710.3 | 14 | MANE Select | |
| Ensembl | ENSP00000498695.1 | 5 | Standard | |
| Ensembl | ENSP00000529358.1 | 14 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| psd2 | Danio rerio | Structure: trunk Quality: curved ventral abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Endocytosis - Homo sapiens (human)
Biological Process
- regulation of ARF protein signal transduction
Molecular Function
- ARF guanyl-nucleotide exchange factor activity
- phospholipid binding
Cellular Component
- integral component of membrane
- dendrite
- cleavage furrow
- ruffle membrane
- neuronal cell body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000274710
- Coding exons
- 14
- Length
- 48646
- Individuals with no LoFs
- 125649
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 99
- Defined
- 125748
- p
- 0.000394
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.430 | 456 | 483 | 0.945 | 0.0000301 | 5054 |
| Missense (PolyPhen) | 169 | 194.58 | 0.86853 | 2052 | ||
| Synonymous | 0.376 | 203 | 210 | 0.967 | 0.0000136 | 1583 |
| Loss of Function | 3.27 | 12 | 32.0 | 0.376 | 0.00000171 | 369 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00012 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.00074 | 0.00069 | rare |
| European (Non-Finnish) | 0.00065 | 0.00062 | rare |
| South Asian | 0.000034 | 0.000033 | rare |
| Other | 0.00051 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- LoFtool
- 0.490
- RVIS EVS
- 0.01
- RVIS percentile EVS
- 54.12
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.699
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |