PHETA1
protein-codingPH domain containing endocytic trafficking adaptor 1, the group of Pleckstrin homology domain containing
Gene summary
This gene encodes a protein that localizes to the endosome and interacts with the enzyme, inositol polyphosphate 5-phosphatase OCRL-1. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
- FAM109A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.5 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 PHETA1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_144671.6. 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 | 49 | 2 | 51 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 49 | 2 | 0 | 51 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_653272.2 | 1 | MANE Select | |
| Ensembl | ENSP00000507123.1 | 1 | MANE Select | |
| RefSeq | NP_001171467.1 | 2 | Standard | |
| RefSeq | NP_001171468.1 | 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
- ENST00000361483
- Coding exons
- 2
- Length
- 8471
- Individuals with no LoFs
- 124865
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 15
- Defined
- 124880
- p
- 0.0000601
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.705 | 154 | 181 | 0.852 | 0.0000136 | 1627 |
| Missense (PolyPhen) | 52 | 68.391 | 0.76034 | 575 | ||
| Synonymous | -0.0341 | 83 | 82.6 | 1.00 | 0.00000630 | 617 |
| Loss of Function | 0.357 | 3 | 3.75 | 0.801 | 1.59e-7 | 44 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00028 | 0.00027 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.00010 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
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}.;
Essentials
- Essential (gene trap)
- N