DPF3

double PHD fingers 3, the group of PHD finger proteins|BAF complex

Basic information

Region (hg38): 14:72609033-72894101

Links

ENSG00000205683 ∙ NCBI:8110 ∙ OMIM:601672 ∙ HGNC:17427 ∙ Uniprot:Q92784 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DPF3 gene.

• Inborn genetic diseases (14 variants)
• not provided (1 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	14	0	1

Variants in DPF3

This is a list of pathogenic ClinVar variants found in the DPF3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-72671162-T-C		not specified	Uncertain significance (Mar 04, 2024)
14-72671220-C-G		not specified	Uncertain significance (Jan 18, 2023)
14-72671281-G-A		not specified	Uncertain significance (Sep 27, 2021)
14-72671303-C-A		not specified	Uncertain significance (Aug 23, 2021)
14-72674258-C-T		not specified	Uncertain significance (Jan 03, 2024)
14-72674282-G-A		not specified	Uncertain significance (Dec 31, 2023)
14-72674300-T-A		not specified	Uncertain significance (Sep 13, 2023)
14-72674302-T-C		not specified	Uncertain significance (Jan 03, 2024)
14-72674356-G-A		not specified	Uncertain significance (Mar 01, 2023)
14-72693141-T-A		not specified	Uncertain significance (Jan 09, 2024)
14-72714438-G-A		not specified	Uncertain significance (Mar 07, 2024)
14-72714445-G-T		not specified	Uncertain significance (Feb 21, 2024)
14-72714495-C-T		not specified	Uncertain significance (Nov 02, 2023)
14-72714498-G-A		not specified	Uncertain significance (Feb 27, 2023)
14-72723635-G-A		not specified	Uncertain significance (Mar 21, 2023)
14-72723725-C-T		not specified	Uncertain significance (Apr 15, 2022)
14-72731810-T-C		not specified	Uncertain significance (May 27, 2022)
14-72753294-G-C		not specified	Uncertain significance (Apr 07, 2023)
14-72753296-T-A		not specified	Uncertain significance (Dec 05, 2022)
14-72753312-A-G			Benign (Jun 27, 2018)
14-72753327-G-A		not specified	Uncertain significance (Dec 17, 2023)
14-72771772-T-C		not specified	Uncertain significance (Sep 16, 2021)
14-72771817-C-T		not specified	Uncertain significance (Jan 24, 2023)
14-72771850-T-G		not specified	Uncertain significance (Jan 10, 2023)
14-72771886-C-T		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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