DESI2

desumoylating isopeptidase 2, the group of Desumoylating isopeptidases

Basic information

Region (hg38): 1:244653103-244709033

Previous symbols: [ "C1orf121", "FAM152A", "PPPDE1" ]

Links

ENSG00000121644 ∙ NCBI:51029 ∙ OMIM:614638 ∙ HGNC:24264 ∙ Uniprot:Q9BSY9 ∙ 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 DESI2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DESI2 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in DESI2

This is a list of pathogenic ClinVar variants found in the DESI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-244686643-A-G		not specified	Uncertain significance (Mar 04, 2024)
1-244689300-C-G		not specified	Uncertain significance (May 26, 2023)
1-244691910-C-G		not specified	Uncertain significance (Nov 03, 2023)
1-244705573-G-T		not specified	Uncertain significance (Apr 04, 2024)
1-244705656-C-T		not specified	Uncertain significance (Jul 14, 2024)
1-244705676-A-G		not specified	Uncertain significance (Nov 22, 2024)
1-244705727-G-A		not specified	Uncertain significance (Dec 14, 2023)
1-244705772-C-T		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DESI2	protein_coding	protein_coding	ENST00000302550	5	56099

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.848	0.151	123593	0	2	123595	0.00000809

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.91	52	108	0.482	0.00000578	1260
Missense in Polyphen		9	35.93	0.25049		434
Synonymous	0.311	40	42.6	0.939	0.00000260	375
Loss of Function	2.73	1	10.6	0.0946	5.12e-7	130

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)	0.0000178	0.0000178
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has deubiquitinating activity towards 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. Deubiquitinates 'Lys-48'- linked polyubiquitination of RPS7 leading to its stabilization (PubMed:28483520). {ECO:0000269|PubMed:28483520}.

Recessive Scores

• pRec: 0.0726

Intolerance Scores

• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.72

Haploinsufficiency Scores

• pHI: 0.116
• hipred: Y
• hipred_score: 0.673
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Desi2
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: desi2
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curved ventral

Gene ontology

• Biological process: protein K63-linked deubiquitination;protein K48-linked deubiquitination
• Cellular component: cytoplasm
• Molecular function: protein binding;thiol-dependent ubiquitinyl hydrolase activity;Lys63-specific deubiquitinase activity;Lys48-specific deubiquitinase activity