PHF24
protein-codingPHD finger protein 24, the group of PHD finger proteins
Gene summary
Predicted to enable transcription corepressor activity. Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to act upstream of or within several processes, including detection of mechanical stimulus involved in sensory perception of pain; gamma-aminobutyric acid signaling pathway; and regulation of GABAergic synaptic transmission. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jun 2026]
- KIAA1045
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~24.9 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 PHF24 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015297.3. 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 | 1 | 1 | ||||
| missense | 62 | 2 | 64 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 63 | 2 | 0 | 65 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056112.1 | 7 | MANE Select | |
| Ensembl | ENSP00000242315.3 | 7 | MANE Select | |
| RefSeq | NP_001291262.1 | 7 | Standard | |
| RefSeq | NP_001334911.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- gamma-aminobutyric acid signaling pathway
- regulation of G protein-coupled receptor signaling pathway
- regulation of synaptic transmission, GABAergic
- detection of mechanical stimulus involved in sensory perception of pain
Molecular Function
- metal ion binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000242315
- Coding exons
- 7
- Length
- 25058
- Individuals with no LoFs
- 124789
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 124802
- p
- 0.0000521
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.721 | 231 | 264 | 0.875 | 0.0000174 | 2609 |
| Missense (PolyPhen) | 75 | 104.69 | 0.71643 | 1082 | ||
| Synonymous | 0.193 | 95 | 97.4 | 0.975 | 0.00000564 | 808 |
| Loss of Function | 3.05 | 6 | 21.1 | 0.284 | 0.00000137 | 196 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000059 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.000071 | 0.000071 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00034 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- -0.34
- RVIS percentile EVS
- 30.56
Essentials
- Essential (gene trap)
- N