DPF2

double PHD fingers 2, the group of PHD finger proteins|BAF complex

Basic information

Region (hg38): 11:65333843-65354262

Previous symbols: [ "REQ" ]

Links

ENSG00000133884 ∙ NCBI:5977 ∙ OMIM:601671 ∙ HGNC:9964 ∙ Uniprot:Q92785 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Coffin-Siris syndrome 7 (Moderate), mode of inheritance: AD
• Coffin-Siris syndrome 7 (Strong), mode of inheritance: AD
• Coffin-Siris syndrome (Supportive), mode of inheritance: AD
• Coffin-Siris syndrome 7 (Strong), mode of inheritance: AD
• Coffin-Siris syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Coffin-Siris syndrome 7	AD	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Craniofacial; Cardiovascular; Musculoskeletal; Neurologic	29429572

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DPF2 gene.

• Coffin-Siris syndrome 7 (3 variants)
• not provided (2 variants)
• Coffin-Siris syndrome 1 (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPF2 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			3	35	3	41
missense	4	6	53	5	3	71
nonsense						0
start loss						0
frameshift		1				1
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1		1			2
splice region			2	10	1	13
non coding			2	28	4	34
Total	5	7	60	68	10

Variants in DPF2

This is a list of pathogenic ClinVar variants found in the DPF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65333844-C-G			Benign (May 21, 2021)
11-65333894-C-G		Autism spectrum disorder	Likely benign (Apr 13, 2022)
11-65333895-T-G		DPF2-related disorder	Likely benign (Jan 17, 2024)
11-65333905-A-G		DPF2-related disorder	Uncertain significance (Jul 18, 2023)
11-65333907-T-C		DPF2-related disorder	Benign/Likely benign (Jan 01, 2024)
11-65333909-T-C		Developmental disorder	Likely benign (Mar 04, 2021)
11-65333910-A-C			Likely benign (Jul 12, 2023)
11-65333916-G-A			Likely benign (Oct 10, 2023)
11-65333921-G-A			Likely benign (Jul 14, 2023)
11-65333929-G-C			Likely benign (Jan 26, 2023)
11-65333933-C-A			Likely benign (Sep 21, 2023)
11-65333935-TTCTC-T			Likely benign (Sep 30, 2022)
11-65333937-C-T			Likely benign (Mar 27, 2023)
11-65340372-A-G			Likely benign (Jun 28, 2022)
11-65340389-G-A		DPF2-related disorder	Uncertain significance (Mar 25, 2024)
11-65340391-G-A			Likely benign (Aug 03, 2023)
11-65340403-C-T			Likely benign (Nov 15, 2023)
11-65340420-A-T			Uncertain significance (Jan 09, 2024)
11-65340429-A-G		Inborn genetic diseases	Uncertain significance (Jun 05, 2024)
11-65340442-C-T		DPF2-related disorder	Benign (Feb 01, 2024)
11-65340457-C-T		DPF2-related disorder	Likely benign (Apr 26, 2023)
11-65340465-G-A			Uncertain significance (Oct 03, 2023)
11-65340490-C-T			Likely benign (Nov 07, 2023)
11-65340504-G-A			Uncertain significance (Aug 10, 2022)
11-65340507-A-G			Uncertain significance (Jul 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPF2	protein_coding	protein_coding	ENST00000528416	11	19496

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000154	125260	0	2	125262	0.00000798

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.90	117	245	0.478	0.0000151	2550
Missense in Polyphen		16	74.801	0.2139		729
Synonymous	-0.243	96	93.0	1.03	0.00000541	732
Loss of Function	4.86	1	29.4	0.0340	0.00000202	277

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000886	0.00000886
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a transcription factor required for the apoptosis response following survival factor withdrawal from myeloid cells. Might also have a role in the development and maturation of lymphoid cells.
• Pathway: Tumor suppressor activity of SMARCB1;b cell survival pathway;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.413
• hipred: Y
• hipred_score: 0.775
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.935

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dpf2
• Phenotype: renal/urinary system phenotype; limbs/digits/tail phenotype; reproductive system phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype

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;apoptotic signaling pathway;negative regulation of myeloid progenitor cell differentiation
• Cellular component: histone acetyltransferase complex;nuclear chromatin;nucleus;nucleoplasm;centrosome;cytosol;intracellular membrane-bounded organelle;nBAF complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;histone acetyltransferase activity;protein binding;histone binding;metal ion binding;H3K9me3 modified histone binding;lysine-acetylated histone binding