DDI2

DNA damage inducible 1 homolog 2, the group of Peptidase family A28

Basic information

Region (hg38): 1:15617458-15669044

Links

ENSG00000197312 ∙ NCBI:84301 ∙ ∙ HGNC:24578 ∙ Uniprot:Q5TDH0 ∙ 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 DDI2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDI2 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		2
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			33	5		38
Total	0	0	40	6	0

Variants in DDI2

This is a list of pathogenic ClinVar variants found in the DDI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-15617675-T-A		not specified	Uncertain significance (Aug 21, 2024)
1-15617760-C-T			Uncertain significance (Mar 01, 2023)
1-15630337-T-C		not specified	Uncertain significance (Jul 06, 2021)
1-15630378-C-T		not specified	Uncertain significance (Oct 29, 2024)
1-15630385-G-A		not specified	Uncertain significance (Nov 10, 2024)
1-15630406-A-T		not specified	Uncertain significance (Dec 05, 2024)
1-15630412-A-G		not specified	Uncertain significance (Jan 04, 2022)
1-15630505-C-G		not specified	Uncertain significance (Jul 14, 2022)
1-15638324-A-C		not specified	Uncertain significance (Nov 08, 2024)
1-15649762-C-G		not specified	Uncertain significance (Aug 28, 2024)
1-15649788-A-G		not specified	Uncertain significance (Apr 07, 2023)
1-15651821-G-A		not specified	Uncertain significance (Oct 24, 2024)
1-15651828-T-C			Likely benign (Mar 01, 2023)
1-15656623-A-G		not specified	Uncertain significance (Sep 26, 2023)
1-15659984-C-T		not specified	Uncertain significance (Aug 14, 2023)
1-15660053-T-G		not specified	Uncertain significance (Dec 13, 2021)
1-15660065-C-A		not specified	Uncertain significance (Dec 04, 2024)
1-15660085-T-C		not specified	Likely benign (Nov 15, 2024)
1-15660092-A-G		not specified	Uncertain significance (Jul 25, 2023)
1-15660106-C-T		not specified	Uncertain significance (Nov 14, 2023)
1-15660125-A-G		not specified	Uncertain significance (Nov 25, 2024)
1-15660179-T-G		not specified	Uncertain significance (Jun 16, 2023)
1-15660197-T-C		not specified	Uncertain significance (Jan 23, 2023)
1-15660215-G-A		not specified	Uncertain significance (May 08, 2023)
1-15660237-T-G		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDI2	protein_coding	protein_coding	ENST00000480945	9	51545

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00181	125657	0	1	125658	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.73	115	232	0.496	0.0000129	2591
Missense in Polyphen		26	89.987	0.28893		1072
Synonymous	-0.909	94	83.4	1.13	0.00000420	793
Loss of Function	4.23	1	22.8	0.0438	0.00000139	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Aspartic protease that mediates the cleavage of NFE2L1/NRF1 at 'Leu-104', thereby promoting release of NFE2L1/NRF1 from the endoplasmic reticulum membrane (PubMed:27676298, PubMed:27528193). Ubiquitination of NFE2L1/NRF1 is a prerequisite for cleavage, suggesting that DDI2 specifically recognizes and binds ubiquitinated NFE2L1/NRF1 (PubMed:27528193). {ECO:0000269|PubMed:27528193, ECO:0000269|PubMed:27676298}.

Intolerance Scores

• loftool: 0.224
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.196
• hipred: Y
• hipred_score: 0.825
• ghis: 0.594

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.418

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddi2

Gene ontology

• Biological process: protein processing
• Cellular component: nucleoplasm;cytosol
• Molecular function: aspartic-type endopeptidase activity;protein binding;identical protein binding;ubiquitin binding