DEK

DEK proto-oncogene, the group of B-WICH chromatin-remodelling complex subunits

Basic information

Region (hg38): 6:18223860-18264548

Links

ENSG00000124795 ∙ NCBI:7913 ∙ OMIM:125264 ∙ HGNC:2768 ∙ Uniprot:P35659 ∙ 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 DEK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEK 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						0
missense			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in DEK

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

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

Position	Type	Phenotype	Significance	ClinVar
6-18225727-T-C		not specified	Uncertain significance (Sep 10, 2024)
6-18226223-G-A		not specified	Uncertain significance (Mar 08, 2024)
6-18236466-G-C		not specified	Uncertain significance (Jun 09, 2022)
6-18236498-G-T		not specified	Uncertain significance (Oct 20, 2021)
6-18237383-T-G		not specified	Uncertain significance (Aug 13, 2021)
6-18237407-T-C		not specified	Uncertain significance (Oct 07, 2024)
6-18237437-T-C		not specified	Uncertain significance (Mar 01, 2024)
6-18237442-A-T		not specified	Uncertain significance (May 02, 2024)
6-18237479-T-G		not specified	Uncertain significance (Nov 28, 2024)
6-18249706-T-C		not specified	Uncertain significance (Oct 06, 2024)
6-18249790-C-T		not specified	Uncertain significance (May 05, 2023)
6-18255778-C-G		not specified	Uncertain significance (Jul 06, 2021)
6-18258349-T-C		not specified	Uncertain significance (Feb 21, 2024)
6-18258391-C-T		not specified	Uncertain significance (Jan 04, 2022)
6-18263846-T-C		not specified	Uncertain significance (May 26, 2022)
6-18263868-G-C		not specified	Likely benign (Oct 14, 2023)
6-18263873-C-T		not specified	Uncertain significance (Oct 08, 2024)
6-18263888-C-T		not specified	Uncertain significance (Dec 10, 2024)
6-18263903-T-C		not specified	Uncertain significance (Dec 28, 2023)
6-18263909-C-T		not specified	Uncertain significance (Jul 19, 2023)
6-18263956-T-C		not specified	Uncertain significance (Aug 23, 2021)
6-18263971-G-A		not specified	Uncertain significance (Mar 01, 2023)
6-18263980-G-A		not specified	Uncertain significance (Oct 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEK	protein_coding	protein_coding	ENST00000397239	10	40956

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.131	0.869	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.404	163	178	0.915	0.00000812	2502
Missense in Polyphen		44	63.041	0.69795		1013
Synonymous	-0.505	68	62.9	1.08	0.00000301	610
Loss of Function	2.91	5	18.5	0.270	8.58e-7	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000924	0.0000923
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000921	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in chromatin organization. {ECO:0000269|PubMed:17524367}.
• Disease: DISEASE: Note=A chromosomal aberration involving DEK is found in a subset of acute myeloid leukemia (AML); also known as acute non- lymphocytic leukemia (PubMed:1549122). Translocation t(6;9)(p23;q34) with NUP214/CAN (PubMed:1549122). It results in the formation of a DEK-NUP214 fusion gene (PubMed:1549122). {ECO:0000269|PubMed:1549122}.
• Pathway: B-WICH complex positively regulates rRNA expression;Positive epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors (Consensus)

Intolerance Scores

• loftool: 0.879
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.898
• hipred: Y
• hipred_score: 0.758
• ghis: 0.667

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dek
• Phenotype: homeostasis/metabolism phenotype; neoplasm

Gene ontology

• Biological process: chromatin organization;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;signal transduction;viral genome replication;positive regulation of gene expression, epigenetic;regulation of double-strand break repair;regulation of double-strand break repair via nonhomologous end joining
• Cellular component: nucleus;nucleoplasm;contractile fiber
• Molecular function: DNA binding;RNA binding;histone binding