PHLDB3
protein-codingpleckstrin homology like domain family B member 3, the group of Pleckstrin homology domain containing
Gene summary
Enables enzyme binding activity. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~30.6 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 PHLDB3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_198850.4. 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 | 1 | 1 | 3 | ||
| missense | 139 | 5 | 2 | 146 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 146 | 6 | 3 | 155 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_942147.3 | 15 | MANE Select | |
| Ensembl | ENSP00000292140.5 | 15 | MANE Select | |
| Ensembl | ENSP00000473248.1 | 2 | Standard | |
| Ensembl | ENSP00000469372.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- TCR
Molecular Function
- enzyme binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000292140
- Coding exons
- 15
- Length
- 29982
- Individuals with no LoFs
- 125333
- Homozygous LoFs
- 3
- Heterozygous LoFs
- 272
- Defined
- 125608
- p
- 0.00110
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.399 | 414 | 392 | 1.06 | 0.0000250 | 3993 |
| Missense (PolyPhen) | 121 | 115.59 | 1.0468 | 1199 | ||
| Synonymous | -0.0149 | 151 | 151 | 1.00 | 0.00000831 | 1302 |
| Loss of Function | 0.419 | 33 | 35.7 | 0.924 | 0.00000197 | 381 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.0024 | 0.0023 | notable |
| Ashkenazi Jewish | 0.00038 | 0.00030 | rare |
| East Asian | 0.00035 | 0.00033 | rare |
| Finnish | 0.000049 | 0.000046 | rare |
| European (Non-Finnish) | 0.00054 | 0.00051 | rare |
| South Asian | 0.0040 | 0.0038 | notable |
| Other | 0.0012 | 0.0011 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.967
- RVIS EVS
- 0.05
- RVIS percentile EVS
- 57.52
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0900
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |