SENP5

SUMO specific peptidase 5, the group of SUMO specific peptidases

Basic information

Region (hg38): 3:196867856-196934714

Links

ENSG00000119231 ∙ NCBI:205564 ∙ OMIM:612845 ∙ HGNC:28407 ∙ Uniprot:Q96HI0 ∙ 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 SENP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SENP5 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			49	1	2	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	49	1	3

Variants in SENP5

This is a list of pathogenic ClinVar variants found in the SENP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-196885222-A-C		not specified	Uncertain significance (Jul 09, 2021)
3-196885287-C-T		not specified	Uncertain significance (Jul 08, 2024)
3-196885322-A-G			Benign (Jun 21, 2018)
3-196885387-C-T		not specified	Uncertain significance (May 16, 2022)
3-196885390-G-C		not specified	Uncertain significance (Aug 12, 2024)
3-196885405-C-T		not specified	Uncertain significance (Mar 08, 2025)
3-196885429-A-G			Benign (Jun 21, 2018)
3-196885465-A-C		not specified	Uncertain significance (Sep 09, 2024)
3-196885482-G-A		not specified	Likely benign (Jun 07, 2023)
3-196885516-T-G		not specified	Uncertain significance (Jun 22, 2023)
3-196885537-T-C		not specified	Uncertain significance (Aug 28, 2024)
3-196885543-C-T		not specified	Uncertain significance (Feb 10, 2025)
3-196885576-G-C		not specified	Uncertain significance (Apr 15, 2024)
3-196885580-G-C		not specified	Uncertain significance (Dec 12, 2024)
3-196885612-C-A		not specified	Uncertain significance (Nov 09, 2023)
3-196885618-A-G		not specified	Uncertain significance (Oct 04, 2022)
3-196885638-A-C		not specified	Uncertain significance (Sep 22, 2022)
3-196885663-C-T		not specified	Uncertain significance (Jan 29, 2025)
3-196885683-A-T		not specified	Uncertain significance (Jun 29, 2023)
3-196885693-A-G		not specified	Uncertain significance (Oct 14, 2021)
3-196885773-G-A		not specified	Uncertain significance (Apr 25, 2023)
3-196885806-G-C		not specified	Uncertain significance (Mar 02, 2023)
3-196885843-A-G		not specified	Likely benign (Mar 01, 2025)
3-196885845-C-T		not specified	Uncertain significance (Aug 04, 2021)
3-196885949-G-C		not specified	Uncertain significance (Mar 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SENP5	protein_coding	protein_coding	ENST00000323460	9	66859

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000217	125728	0	11	125739	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	277	395	0.700	0.0000198	5044
Missense in Polyphen		56	152.05	0.3683		1964
Synonymous	-0.0302	145	145	1.00	0.00000746	1359
Loss of Function	4.99	2	32.9	0.0607	0.00000162	418

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protease that catalyzes two essential functions in the SUMO pathway: processing of full-length SUMO3 to its mature form and deconjugation of SUMO2 and SUMO3 from targeted proteins. Has weak proteolytic activity against full-length SUMO1 or SUMO1 conjugates. Required for cell division. {ECO:0000269|PubMed:16608850, ECO:0000269|PubMed:16738315}.
• Pathway: SUMO is proteolytically processed;Post-translational protein modification;Metabolism of proteins;Processing and activation of SUMO;SUMOylation (Consensus)

Recessive Scores

• pRec: 0.0801

Intolerance Scores

• loftool: 0.275
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.51

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.436
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.112

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Senp5

Gene ontology

• Biological process: cell cycle;protein sumoylation;protein desumoylation;cell division
• Cellular component: nucleus;nucleoplasm;nucleolus
• Molecular function: protein binding;SUMO-specific endopeptidase activity