PHF19
protein-codingPHD finger protein 19, the group of PHD finger proteins|Tudor domain containing
Gene summary
Enables histone H3K36me3 reader activity. Involved in negative regulation of gene expression, epigenetic. Part of ESC/E(Z) complex. [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 ~39.2 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 PHF19 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015651.3. 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 | 48 | 1 | 49 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 51 | 1 | 0 | 52 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056466.1 | 14 | MANE Select | |
| Ensembl | ENSP00000363003.3 | 14 | MANE Select | |
| RefSeq | NP_001009936.1 | 4 | Standard | |
| RefSeq | NP_001273769.1 | 15 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Epigenetic regulation of gene expression
- Gene expression (Transcription)
- PRC2 methylates histones and DNA
Biological Process
- chromatin organization
- negative regulation of gene expression, epigenetic
- positive regulation of transcription, DNA-templated
- positive regulation of histone H3-K27 methylation
Molecular Function
- DNA-binding transcription factor activity
- protein binding
- nucleosome binding
- methylated histone binding
- sequence-specific DNA binding
Cellular Component
- nucleoplasm
- ESC/E(Z) complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000373896
- Coding exons
- 14
- Length
- 21630
- Individuals with no LoFs
- 125743
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 125748
- p
- 0.0000199
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.35 | 166 | 340 | 0.489 | 0.0000202 | 3754 |
| Missense (PolyPhen) | 30 | 118.42 | 0.25334 | 1229 | ||
| Synonymous | 0.981 | 123 | 138 | 0.894 | 0.00000810 | 1111 |
| Loss of Function | 5.00 | 3 | 34.9 | 0.0859 | 0.00000190 | 380 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000035 | 0.000035 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Polycomb group (PcG) that specifically binds histone H3 trimethylated at 'Lys-36' (H3K36me3) and recruits the PRC2 complex. Probably involved in the transition from an active state to a repressed state in embryonic stem cells: acts by binding to H3K36me3, a mark for transcriptional activation, and recruiting H3K36me3 histone demethylases RIOX1 or KDM2B, leading to demethylation of H3K36 and recruitment of the PRC2 complex that mediates H3K27me3 methylation, followed by de novo silencing. Recruits the PRC2 complex to CpG islands and contributes to embryonic stem cell self-renewal. Also binds dimethylated at 'Lys- 36' (H3K36me2). Isoform 1 and isoform 2 inhibit transcription from an HSV-tk promoter. {ECO:0000269|PubMed:15563832, ECO:0000269|PubMed:21143197, ECO:0000269|PubMed:23104054, ECO:0000269|PubMed:23160351}.;
Recessive Scores
- pRec
- 0.123
Intolerance Scores
- LoFtool
- 0.154
- RVIS EVS
- 0.02
- RVIS percentile EVS
- 55.61
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |