DAP3

death associated protein 3, the group of Mitochondrial ribosomal proteins

Basic information

Region (hg38): 1:155687960-155739010

Links

ENSG00000132676 ∙ NCBI:7818 ∙ OMIM:602074 ∙ HGNC:2673 ∙ Uniprot:P51398 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Perrault syndrome 7	AR	Audiologic/Otolaryngologic	Hearing loss has been described in early childhood, and early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Neurologic; Obstetric	39701103

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DAP3 gene.

• not_specified (50 variants)
• not_provided (4 variants)
• Perrault_syndrome_1 (3 variants)
• Perrault_syndrome_7 (3 variants)
• DAP3-related_disorder (1 variants)
• See_cases (1 variants)

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. These statistics are base on transcript: NM_000004632.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense		3	44	6	1	54
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	3	44	7	1

Highest pathogenic variant AF is 0.0000024780015

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