DPF3
double PHD fingers 3, the group of PHD finger proteins|BAF complex
Basic information
Region (hg38): 14:72609034-72894101
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (48 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPF3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001280542.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 41 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 41 | 0 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DPF3 | protein_coding | protein_coding | ENST00000541685 | 9 | 274806 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0205 | 0.979 | 124652 | 0 | 23 | 124675 | 0.0000922 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.15 | 181 | 230 | 0.787 | 0.0000149 | 2322 |
| Missense in Polyphen | 34 | 48.718 | 0.69789 | 392 | ||
| Synonymous | -0.460 | 93 | 87.5 | 1.06 | 0.00000595 | 671 |
| Loss of Function | 2.97 | 7 | 22.1 | 0.317 | 0.00000143 | 235 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000279 | 0.000279 |
| Ashkenazi Jewish | 0.0000994 | 0.0000993 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000465 | 0.0000464 |
| European (Non-Finnish) | 0.0000806 | 0.0000796 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000132 | 0.000131 |
| Other | 0.000166 | 0.000165 |
dbNSFP
Source:
- Function
- FUNCTION: Belongs to the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Muscle-specific component of the BAF complex, a multiprotein complex involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Specifically binds acetylated lysines on histone 3 and 4 (H3K14ac, H3K9ac, H4K5ac, H4K8ac, H4K12ac, H4K16ac). In the complex, it acts as a tissue-specific anchor between histone acetylations and methylations and chromatin remodeling. It thereby probably plays an essential role in heart and skeletal muscle development. {ECO:0000250, ECO:0000269|PubMed:18765789}.;
- Pathway
- Thermogenesis - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Tumor suppressor activity of SMARCB1
(Consensus)
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.447
- rvis_EVS
- -0.54
- rvis_percentile_EVS
- 20.54
Haploinsufficiency Scores
- pHI
- 0.480
- hipred
- Y
- hipred_score
- 0.814
- ghis
- 0.599
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.113
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dpf3
- Phenotype
- normal phenotype;
Zebrafish Information Network
- Gene name
- dpf3
- Affected structure
- cardiac muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- disorganized
Gene ontology
- Biological process
- nervous system development;biological_process;histone acetylation;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
- Cellular component
- histone acetyltransferase complex;nuclear chromatin;nucleus;nucleoplasm;nBAF complex
- Molecular function
- nucleic acid binding;histone acetyltransferase activity;zinc ion binding;histone binding