SENP8

SUMO peptidase family member, NEDD8 specific, the group of SUMO specific peptidases

Basic information

Region (hg38): 15:72114258-72143692

Previous symbols: [ "PRSC2" ]

Links

ENSG00000166192 ∙ NCBI:123228 ∙ OMIM:608659 ∙ HGNC:22992 ∙ Uniprot:Q96LD8 ∙ 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 SENP8 gene.

• not_specified (13 variants)
• Neurodevelopmental_abnormality (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SENP8 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000145204.4. 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						0
missense			13			13
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	14	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SENP8	protein_coding	protein_coding	ENST00000544411	1	26713

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000547	0.479	125717	0	21	125738	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	70	107	0.652	0.00000534	1421
Missense in Polyphen		16	30.275	0.5285		451
Synonymous	-1.03	53	44.3	1.20	0.00000256	388
Loss of Function	0.191	5	5.48	0.912	2.36e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000114
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protease that catalyzes two essential functions in the NEDD8 pathway: processing of full-length NEDD8 to its mature form and deconjugation of NEDD8 from targeted proteins such as cullins or p53. {ECO:0000269|PubMed:12730221, ECO:0000269|PubMed:12759362, ECO:0000269|PubMed:12759363, ECO:0000269|PubMed:15242646, ECO:0000269|PubMed:15775960}.
• Pathway: Post-translational protein modification;Metabolism of proteins;UCH proteinases;Neddylation;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.616
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.159
• hipred: Y
• hipred_score: 0.730
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Senp8

Gene ontology

• Biological process: protein deubiquitination;post-translational protein modification
• Cellular component: cytosol
• Molecular function: NEDD8-specific protease activity