PHETA2
protein-codingPH domain containing endocytic trafficking adaptor 2, the group of Pleckstrin homology domain containing
Gene summary
Enables protein homodimerization activity. Involved in endosome organization; receptor recycling; and retrograde transport, endosome to Golgi. Located in cytoplasmic vesicle and trans-Golgi network. [provided by Alliance of Genome Resources, Jul 2025]
- FAM109B
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.2 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 PHETA2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001002034.3. 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 | 0 | |||||
| missense | 38 | 2 | 40 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 38 | 2 | 0 | 40 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001002034.2 | 1 | MANE Select | |
| Ensembl | ENSP00000312753.3 | 1 | MANE Select | |
| Ensembl | ENSP00000396170.1 | 1 | Standard | |
| Ensembl | ENSP00000574293.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- receptor recycling
- endosome organization
- retrograde transport, endosome to Golgi
Molecular Function
- protein binding
- protein homodimerization activity
Cellular Component
- early endosome
- trans-Golgi network
- cytosol
- clathrin-coated vesicle
- recycling endosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000321753
- Coding exons
- 1
- Length
- 5191
- Individuals with no LoFs
- 125530
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 204
- Defined
- 125735
- p
- 0.000816
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.825 | 132 | 162 | 0.817 | 0.0000103 | 1653 |
| Missense (PolyPhen) | 61 | 64.541 | 0.94514 | 680 | ||
| Synonymous | 0.858 | 60 | 69.1 | 0.869 | 0.00000424 | 555 |
| Loss of Function | -0.203 | 8 | 7.40 | 1.08 | 4.88e-7 | 63 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0073 | 0.0071 | notable |
| Latino/Admixed American | 0.00046 | 0.00043 | rare |
| Ashkenazi Jewish | 0.00012 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.0022 | 0.0022 | notable |
| European (Non-Finnish) | 0.00018 | 0.00018 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00052 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in endocytic trafficking. Required for receptor recycling from endosomes, both to the trans-Golgi network and the plasma membrane. {ECO:0000269|PubMed:21233288}.;
Intolerance Scores
- RVIS EVS
- 0.19
- RVIS percentile EVS
- 67.03
Essentials
- Essential (gene trap)
- N