DPF1

double PHD fingers 1, the group of BAF complex|PHD finger proteins

Basic information

Region (hg38): 19:38211005-38229714

Links

ENSG00000011332 ∙ NCBI:8193 ∙ OMIM:601670 ∙ HGNC:20225 ∙ Uniprot:Q92782 ∙ 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 DPF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPF1 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	11	1	0

Variants in DPF1

This is a list of pathogenic ClinVar variants found in the DPF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-38212079-T-G		not specified	Uncertain significance (Jun 05, 2024)
19-38212089-C-A		not specified	Uncertain significance (Jan 03, 2024)
19-38216181-C-T		not specified	Uncertain significance (Apr 12, 2022)
19-38217477-C-A		not specified	Uncertain significance (Dec 20, 2021)
19-38217496-G-T		not specified	Uncertain significance (Mar 21, 2022)
19-38217506-G-A			Likely benign (Oct 01, 2022)
19-38218610-T-C		not specified	Uncertain significance (Jan 03, 2024)
19-38218625-A-T		not specified	Uncertain significance (Jun 16, 2024)
19-38218640-G-A		not specified	Uncertain significance (Oct 05, 2023)
19-38218964-C-A		not specified	Uncertain significance (Apr 25, 2022)
19-38222455-G-A		not specified	Uncertain significance (Sep 26, 2023)
19-38222458-G-T		not specified	Uncertain significance (Oct 03, 2023)
19-38224159-T-G		not specified	Uncertain significance (Dec 06, 2022)
19-38224177-G-T		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPF1	protein_coding	protein_coding	ENST00000355526	12	18709

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.00951	125730	0	6	125736	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.07	119	258	0.461	0.0000165	2680
Missense in Polyphen		25	93.039	0.2687		891
Synonymous	0.668	105	114	0.920	0.00000831	760
Loss of Function	4.30	3	27.2	0.110	0.00000160	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000462	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have an important role in developing neurons by participating in regulation of cell survival, possibly as a neurospecific transcription factor. 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). {ECO:0000250}.
• Pathway: Thermogenesis - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Tumor suppressor activity of SMARCB1 (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.0483
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.290
• hipred: Y
• hipred_score: 0.789
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.917

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dpf1

Gene ontology

• Biological process: apoptotic process;nervous system development;histone acetylation;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: histone acetyltransferase complex;nuclear chromatin;nucleus;cytoplasm;nBAF complex
• Molecular function: histone acetyltransferase activity;zinc ion binding;histone binding