DAP3

death associated protein 3, the group of Mitochondrial ribosomal proteins

Basic information

Region (hg38): 1:155687959-155739010

Links

ENSG00000132676 ∙ NCBI:7818 ∙ OMIM:602074 ∙ HGNC:2673 ∙ Uniprot:P51398 ∙ 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 DAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DAP3 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			18	3	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	18	4	1

Variants in DAP3

This is a list of pathogenic ClinVar variants found in the DAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-155688070-C-A		Grange syndrome	Likely pathogenic (Mar 26, 2024)
1-155688077-G-A			Likely pathogenic (Nov 16, 2022)
1-155688080-G-A			Benign (Dec 31, 2019)
1-155688099-A-G			Benign (Dec 31, 2019)
1-155688109-G-A		Inborn genetic diseases	Uncertain significance (Apr 17, 2024)
1-155688110-A-G			Benign/Likely benign (May 01, 2024)
1-155688140-G-A		Inborn genetic diseases	Uncertain significance (Feb 28, 2024)
1-155688145-C-T			Benign (Dec 31, 2019)
1-155688191-G-A		Inborn genetic diseases	Uncertain significance (May 27, 2022)
1-155688195-A-T		YY1AP1-related disorder	Likely benign (Aug 14, 2019)
1-155688218-AGAG-A		Grange syndrome	Uncertain significance (Feb 16, 2018)
1-155688221-G-A		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
1-155688224-G-A		YY1AP1-related disorder	Likely benign (Dec 31, 2019)
1-155688235-T-C		Inborn genetic diseases	Likely benign (Oct 14, 2023)
1-155688239-G-A		Inborn genetic diseases	Uncertain significance (Dec 18, 2023)
1-155688244-A-T			Pathogenic (Nov 25, 2017)
1-155688259-G-A		Inborn genetic diseases	Uncertain significance (Sep 14, 2022)
1-155688262-G-A		Inborn genetic diseases	Uncertain significance (Apr 12, 2023)
1-155688269-A-G		Inborn genetic diseases • YY1AP1-related disorder	Benign/Likely benign (Jun 21, 2023)
1-155688285-T-C			Likely benign (Jul 10, 2017)
1-155688290-T-C		Inborn genetic diseases	Uncertain significance (Mar 08, 2024)
1-155688292-G-T		Inborn genetic diseases	Uncertain significance (Feb 06, 2024)
1-155688300-T-TC			Pathogenic (Sep 08, 2017)
1-155688320-GGCGGCGGCA-G		YY1AP1-related disorder	Benign (Dec 31, 2019)
1-155688323-G-A		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DAP3	protein_coding	protein_coding	ENST00000368336	12	51051

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.11e-9	0.532	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.311	206	219	0.941	0.0000116	2616
Missense in Polyphen		38	52.212	0.72781		633
Synonymous	0.127	78	79.4	0.982	0.00000420	746
Loss of Function	1.17	17	23.1	0.737	0.00000108	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00114	0.00113
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.0000545	0.0000544
South Asian	0.000167	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in mediating interferon-gamma-induced cell death.
• Pathway: Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation;TRAIL signaling pathway (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.970
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.43

Haploinsufficiency Scores

• pHI: 0.263
• hipred: N
• hipred_score: 0.394
• ghis: 0.590

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.799

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dap3
• Phenotype: cellular 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); hematopoietic system phenotype; growth/size/body region phenotype; embryo phenotype

Gene ontology

• Biological process: mitochondrial translational elongation;mitochondrial translational termination;apoptotic signaling pathway
• Cellular component: nucleoplasm;mitochondrion;mitochondrial inner membrane;mitochondrial small ribosomal subunit
• Molecular function: RNA binding;structural constituent of ribosome;protein binding;GTP binding