SENP1

SUMO specific peptidase 1, the group of SUMO specific peptidases

Basic information

Region (hg38): 12:48042896-48106079

Links

ENSG00000079387 ∙ NCBI:29843 ∙ OMIM:612157 ∙ HGNC:17927 ∙ Uniprot:Q9P0U3 ∙ 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 SENP1 gene.

• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SENP1 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					2	2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	2

Variants in SENP1

This is a list of pathogenic ClinVar variants found in the SENP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-48065129-T-C			Benign (May 14, 2018)
12-48088943-T-C			Benign (Dec 21, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SENP1	protein_coding	protein_coding	ENST00000004980	17	63411

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00642	124646	0	7	124653	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.00	227	329	0.690	0.0000168	4218
Missense in Polyphen		48	120.79	0.3974		1528
Synonymous	-0.0394	115	114	1.00	0.00000555	1172
Loss of Function	5.11	6	41.5	0.145	0.00000245	464

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000649	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000361	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.000110	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protease that catalyzes two essential functions in the SUMO pathway (PubMed:10652325, PubMed:15199155, PubMed:16253240, PubMed:16553580, PubMed:21829689, PubMed:21965678, PubMed:23160374, PubMed:24943844, PubMed:25406032, PubMed:29506078). The first is the hydrolysis of an alpha-linked peptide bond at the C-terminal end of the small ubiquitin-like modifier (SUMO) propeptides, SUMO1, SUMO2 and SUMO3 leading to the mature form of the proteins. The second is the deconjugation of SUMO1, SUMO2 and SUMO3 from targeted proteins, by cleaving an epsilon-linked peptide bond between the C-terminal glycine of the mature SUMO and the lysine epsilon-amino group of the target protein. Deconjugates SUMO1 from HIPK2 (PubMed:16253240). Deconjugates SUMO1 from HDAC1 and BHLHE40/DEC1, which decreases its transcriptional repression activity (PubMed:21829689). Deconjugates SUMO1 from CLOCK, which decreases its transcriptional activation activity (PubMed:23160374). Deconjugates SUMO2 from MTA1 (PubMed:21965678). Deconjugates SUMO1 from METTL3 (PubMed:29506078). Desumoylates CCAR2 which decreases its interaction with SIRT1 (PubMed:25406032). Deconjugates SUMO1 from GPS2 (PubMed:24943844). {ECO:0000269|PubMed:10652325, ECO:0000269|PubMed:15199155, ECO:0000269|PubMed:16253240, ECO:0000269|PubMed:16553580, ECO:0000269|PubMed:21829689, ECO:0000269|PubMed:21965678, ECO:0000269|PubMed:23160374, ECO:0000269|PubMed:24943844, ECO:0000269|PubMed:25406032, ECO:0000269|PubMed:29506078}.
• Pathway: SUMO is proteolytically processed;Post-translational protein modification;Metabolism of proteins;Processing and activation of SUMO;AndrogenReceptor;SUMOylation;Regulation of Androgen receptor activity (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.228
• hipred: Y
• hipred_score: 0.859
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.958

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Senp1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cellular phenotype; immune system phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: proteolysis;activation of cysteine-type endopeptidase activity involved in apoptotic process;regulation of definitive erythrocyte differentiation;protein sumoylation;protein desumoylation;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;positive regulation of transcription by RNA polymerase II;apoptotic signaling pathway
• Cellular component: nucleus;nucleoplasm;cytoplasm;focal adhesion;nuclear membrane
• Molecular function: endopeptidase activity;protein binding;SUMO-specific endopeptidase activity;SUMO-specific isopeptidase activity