PHF21A: PHD Finger Protein 21A
A chromatin-associated factor implicated in neurodevelopment and cancer
Gene Information Card
| Symbol | PHF21A |
|---|---|
| Full Name | PHD Finger Protein 21A |
| Gene Type | Protein coding |
| Chromosomal Location | 11p11.2 |
| NCBI Gene ID | 51317 ncbi.nlm.nih.gov/gene/51317 |
| Ensembl ID | ENSG00000149294 |
| UniProt ID | Q96BD5 |
| OMIM ID | 608325 |
| HGNC ID | 24105 |
| Aliases | BHC80, BM-006, FLJ20036, KIAA1696 |
Description
PHF21A encodes a PHD finger-containing protein that functions as a component of the BRAF35-HDAC complex (BHC). It acts as a transcriptional repressor by recruiting histone deacetylases and demethylases to target gene promoters. PHF21A is involved in chromatin remodeling, neuronal development, and cell cycle regulation. Loss-of-function mutations are associated with Potocki-Shaffer syndrome and intellectual disability.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Potocki-Shaffer syndrome | Haploinsufficiency of PHF21A due to 11p11.2 deletion leads to craniofacial abnormalities, intellectual disability, and multiple exostoses | OMIM #601224; ClinVar |
| Intellectual disability, autosomal dominant 66 | De novo missense and truncating mutations in PHF21A impair chromatin binding and transcriptional repression | ClinVar; PMID: 31036919 |
| Breast cancer | PHF21A overexpression correlates with poor prognosis; promotes proliferation via HDAC recruitment | COSMIC; PMID: 25652368 |
| Lung cancer | Somatic mutations and copy number gains in PHF21A observed in lung adenocarcinoma | COSMIC; PMID: 29056340 |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 12.5 | Medium |
| Testis | 8.3 | Low |
| Lung | 6.1 | Low |
| Breast | 5.4 | Low |
| Liver | 4.2 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| SH-SY5Y | 14.2 | Neuroblastoma cell line |
| HEK293 | 9.8 | Embryonic kidney |
| MCF7 | 7.5 | Breast cancer |
| A549 | 6.3 | Lung cancer |
| HepG2 | 5.1 | Liver cancer |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1A>G (p.Met1?) | Start loss | <0.1% | Loss of protein expression; associated with intellectual disability |
| c.487C>T (p.Arg163*) | Nonsense | <0.1% | Truncation; loss of PHD finger; Potocki-Shaffer syndrome |
| c.1012G>A (p.Gly338Arg) | Missense | <0.1% | Impaired chromatin binding; dominant negative effect |
| c.1345_1346insA (p.Thr449Asnfs*12) | Frameshift | <0.1% | Loss of C-terminal domain; loss of function |
Mutation functional classification
Loss of Function (LOF)
Nonsense, frameshift, and start-loss mutations that abolish protein expression or truncate key domains (PHD finger) are classified as loss-of-function.
Gain of Function (GOF)
No confirmed gain-of-function mutations reported in PHF21A.
Dominant Negative (DN)
Missense mutations in the PHD finger (e.g., p.Gly338Arg) that disrupt chromatin binding while retaining interaction with HDAC complex may exert dominant-negative effects.
View complete mutation data：
Gene Ontology (GO)
| • Chromatin binding | • Histone deacetylase binding |
| • Transcription corepressor activity | • Nucleus |
| • PHD finger domain | • Negative regulation of transcription by RNA polymerase II |
Pathways
• BRAF35-HDAC complex (BHC) pathway
• Chromatin remodeling
• Transcriptional repression by histone deacetylation
Protein Summary
PHF21A (BHC80) is a 741-amino acid protein containing a plant homeodomain (PHD) finger that recognizes unmethylated histone H3 lysine 4 (H3K4me0). It serves as a scaffold within the BRAF35-HDAC complex, linking histone deacetylase 1/2 (HDAC1/2) and lysine-specific demethylase 1 (LSD1) to target promoters. The protein is essential for neuronal gene silencing and cell cycle control. Mutations disrupting its PHD finger or leading to haploinsufficiency cause neurodevelopmental disorders.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| PHF21A Knockout HEK293 Cell Line | EDJ-KQ11045 | Human | 51317 | Details Get a Quote |
| PHF21A Knockout A-549 Cell Line | EDJ-KQ38952 | Human | 51317 | Details Get a Quote |
| PHF21A Knockout HeLa Cell Line | EDJ-KQ38954 | Human | 51317 | Details Get a Quote |
| PHF21A Knockout HCT 116 Cell Line | EDJ-KQ37645 | Human | 51317 | Details Get a Quote |
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