DEDD2

death effector domain containing 2, the group of Death effector domain containing

Basic information

Region (hg38): 19:42198598-42220140

Links

ENSG00000160570 ∙ NCBI:162989 ∙ OMIM:617078 ∙ HGNC:24450 ∙ Uniprot:Q8WXF8 ∙ 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 DEDD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEDD2 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			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	0	0

Variants in DEDD2

This is a list of pathogenic ClinVar variants found in the DEDD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-42199454-G-A		not specified	Uncertain significance (Sep 25, 2024)
19-42199458-G-A		not specified	Uncertain significance (May 27, 2022)
19-42199461-G-A		not specified	Uncertain significance (Jul 20, 2022)
19-42199467-C-T		not specified	Uncertain significance (Mar 11, 2025)
19-42199472-T-A		not specified	Uncertain significance (Jun 09, 2022)
19-42199493-C-T		not specified	Uncertain significance (Aug 10, 2021)
19-42199551-G-A		not specified	Uncertain significance (Aug 01, 2024)
19-42199588-G-A			Likely benign (Apr 04, 2024)
19-42199728-C-A		not specified	Uncertain significance (Dec 14, 2024)
19-42199739-C-T		not specified	Uncertain significance (Dec 21, 2023)
19-42199757-C-T		not specified	Uncertain significance (Jun 07, 2024)
19-42199798-G-A			Benign (Apr 01, 2025)
19-42199817-C-T		not specified	Uncertain significance (Jan 23, 2025)
19-42199818-G-A		not specified	Uncertain significance (Jan 31, 2023)
19-42209727-G-T		not specified	Uncertain significance (Jan 16, 2024)
19-42209775-G-A		not specified	Uncertain significance (Nov 15, 2024)
19-42209778-G-A		not specified	Uncertain significance (Feb 02, 2022)
19-42209808-G-A		not specified	Uncertain significance (Nov 10, 2022)
19-42209829-T-C		not specified	Uncertain significance (Sep 26, 2024)
19-42209831-G-C		not specified	Uncertain significance (Dec 23, 2024)
19-42215172-T-G		not specified	Uncertain significance (Aug 02, 2023)
19-42215187-G-A		not specified	Uncertain significance (May 13, 2024)
19-42215190-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-42215211-T-C		not specified	Uncertain significance (May 01, 2024)
19-42215219-C-A		not specified	Uncertain significance (Dec 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEDD2	protein_coding	protein_coding	ENST00000595337	4	21543

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0599	0.925	125739	0	6	125745	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	161	216	0.744	0.0000147	1988
Missense in Polyphen		33	50.167	0.65781		489
Synonymous	0.298	87	90.6	0.960	0.00000483	760
Loss of Function	2.12	4	11.9	0.337	6.52e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000477	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a critical role in death receptor-induced apoptosis and may target CASP8 and CASP10 to the nucleus. May regulate degradation of intermediate filaments during apoptosis. May play a role in the general transcription machinery in the nucleus and might be an important regulator of the activity of GTF3C3.
• Pathway: Cellular response to heat stress;HSF1 activation;Attenuation phase;HSF1-dependent transactivation;Regulation of HSF1-mediated heat shock response;Cellular responses to stress;Cellular responses to external stimuli;Cellular response to heat stress (Consensus)

Intolerance Scores

• loftool: 0.117
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.132
• hipred: Y
• hipred_score: 0.658
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.822

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dedd2

Gene ontology

• Biological process: RNA processing;extrinsic apoptotic signaling pathway via death domain receptors;rRNA catabolic process;cellular homeostasis;apoptotic nuclear changes;intracellular signal transduction;negative regulation of transcription, DNA-templated;positive regulation of extrinsic apoptotic signaling pathway
• Cellular component: nucleolus
• Molecular function: DNA binding;protein binding;receptor signaling complex scaffold activity