DAD1

defender against cell death 1, the group of Oligosaccharyltransferase complex subunits

Basic information

Region (hg38): 14:22564907-22589224

Links

ENSG00000129562 ∙ NCBI:1603 ∙ OMIM:600243 ∙ HGNC:2664 ∙ Uniprot:P61803 ∙ 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 DAD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DAD1 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					8	8
Total	0	0	4	0	9

Variants in DAD1

This is a list of pathogenic ClinVar variants found in the DAD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-22574780-AT-A			Benign (Jun 19, 2021)
14-22574793-T-C			Benign (Jun 19, 2021)
14-22574887-A-G			Benign (Jun 19, 2021)
14-22574987-T-A			Benign (Jun 19, 2021)
14-22575104-C-T			Benign (Jun 09, 2021)
14-22575167-G-C		not specified	Uncertain significance (Jul 11, 2023)
14-22575361-A-G			Benign (Jun 19, 2021)
14-22575443-A-G			Benign (Jun 19, 2021)
14-22575540-CA-C			Benign (Jun 19, 2021)
14-22588761-G-C			Benign (Jun 19, 2021)
14-22589093-T-C		not specified	Uncertain significance (Oct 05, 2021)
14-22589135-A-G		not specified	Uncertain significance (Feb 03, 2022)
14-22589138-G-C		not specified	Uncertain significance (Apr 22, 2024)
14-22589147-G-C		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DAD1	protein_coding	protein_coding	ENST00000250498	2	24371

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0855	0.772	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.678	47	62.0	0.758	0.00000283	723
Missense in Polyphen		16	22.65	0.70641		268
Synonymous	1.03	22	29.0	0.758	0.00000139	246
Loss of Function	1.09	2	4.49	0.446	2.75e-7	43

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential subunit of the N-oligosaccharyl transferase (OST) complex which catalyzes the transfer of a high mannose oligosaccharide from a lipid-linked oligosaccharide donor to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains. Required for the assembly of both SST3A- and SS3B-containing OST complexes. Required for efficient N-glycosylation. Loss of the DAD1 protein triggers apoptosis. {ECO:0000269|PubMed:22467853, ECO:0000305}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);N-Glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;Asparagine N-linked glycosylation;N-Glycan biosynthesis (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.487
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.250
• hipred: Y
• hipred_score: 0.804
• ghis: 0.632

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dad1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; embryo phenotype; immune system phenotype; limbs/digits/tail phenotype; hematopoietic system 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)

Gene ontology

• Biological process: blastocyst development;protein glycosylation;protein N-linked glycosylation;apoptotic process;response to nutrient;protein N-linked glycosylation via asparagine;response to drug;negative regulation of apoptotic process
• Cellular component: endoplasmic reticulum membrane;oligosaccharyltransferase complex;membrane;integral component of membrane
• Molecular function: oligosaccharyl transferase activity;dolichyl-diphosphooligosaccharide-protein glycotransferase activity