DESI1

desumoylating isopeptidase 1, the group of Desumoylating isopeptidases

Basic information

Region (hg38): 22:41598028-41621043

Previous symbols: [ "FAM152B", "PPPDE2" ]

Links

ENSG00000100418 ∙ NCBI:27351 ∙ OMIM:614637 ∙ HGNC:24577 ∙ Uniprot:Q6ICB0 ∙ 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 DESI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DESI1 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in DESI1

This is a list of pathogenic ClinVar variants found in the DESI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-41601108-C-T		not specified	Uncertain significance (Feb 07, 2023)
22-41601142-C-G		not specified	Uncertain significance (Dec 21, 2023)
22-41604053-G-A		not specified	Uncertain significance (Sep 20, 2023)
22-41604068-G-A		not specified	Uncertain significance (Oct 25, 2023)
22-41620785-C-T		not specified	Uncertain significance (Mar 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DESI1	protein_coding	protein_coding	ENST00000263256	6	23069

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00571	0.909	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.856	69	92.1	0.749	0.00000486	1075
Missense in Polyphen		18	30.524	0.5897		369
Synonymous	0.0259	38	38.2	0.995	0.00000202	347
Loss of Function	1.47	5	10.0	0.498	6.12e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000153	0.000149
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protease which deconjugates SUMO1, SUMO2 and SUMO3 from some substrate proteins. Has isopeptidase but not SUMO-processing activity. Desumoylates ZBTB46 (By similarity). {ECO:0000250}.

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.642
• hipred: Y
• hipred_score: 0.507
• ghis: 0.615

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Desi1

Gene ontology

• Biological process: proteolysis
• Cellular component: nucleus;cytoplasm
• Molecular function: peptidase activity;identical protein binding