SENP2

SUMO specific peptidase 2, the group of SUMO specific peptidases

Basic information

Region (hg38): 3:185582495-185633551

Links

ENSG00000163904 ∙ NCBI:59343 ∙ OMIM:608261 ∙ HGNC:23116 ∙ Uniprot:Q9HC62 ∙ 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 SENP2 gene.

• Inborn genetic diseases (14 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SENP2 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			14		2	16
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	14	0	2

Variants in SENP2

This is a list of pathogenic ClinVar variants found in the SENP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-185590127-A-G		not specified	Uncertain significance (Aug 02, 2022)
3-185598419-T-G		not specified	Uncertain significance (May 23, 2023)
3-185598513-A-T		not specified	Uncertain significance (Jun 30, 2022)
3-185598986-T-C		not specified	Uncertain significance (Dec 28, 2023)
3-185600834-G-A		not specified	Uncertain significance (Dec 28, 2022)
3-185606409-A-G		not specified	Uncertain significance (Feb 10, 2022)
3-185609326-G-A		not specified	Uncertain significance (Sep 17, 2021)
3-185609340-A-G			Benign (Jul 13, 2018)
3-185611662-G-A		not specified	Uncertain significance (May 06, 2022)
3-185611739-A-G		not specified	Uncertain significance (Jan 04, 2022)
3-185611744-A-T		not specified	Uncertain significance (Feb 06, 2023)
3-185612603-A-G			Likely benign (May 01, 2023)
3-185613377-C-A			Benign (Jul 13, 2018)
3-185614583-A-C		not specified	Uncertain significance (Dec 14, 2022)
3-185617499-G-A		not specified	Uncertain significance (Feb 15, 2023)
3-185617502-A-G		not specified	Uncertain significance (Jul 06, 2021)
3-185617519-C-T		not specified	Uncertain significance (Jan 03, 2024)
3-185617520-C-T		not specified	Uncertain significance (Feb 06, 2023)
3-185619399-C-T		not specified	Uncertain significance (Jan 02, 2024)
3-185629792-C-G		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SENP2	protein_coding	protein_coding	ENST00000296257	17	51056

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0174	125729	0	12	125741	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.87	221	314	0.703	0.0000159	3869
Missense in Polyphen		51	96.309	0.52954		1186
Synonymous	0.559	100	107	0.931	0.00000523	1086
Loss of Function	4.88	6	38.8	0.155	0.00000225	445

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000163	0.000109
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protease that catalyzes two essential functions in the SUMO pathway. 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. May down-regulate CTNNB1 levels and thereby modulate the Wnt pathway. Deconjugates SUMO2 from MTA1. Plays a dynamic role in adipogenesis by desumoylating and promoting the stabilization of CEBPB (PubMed:20194620). {ECO:0000250|UniProtKB:Q91ZX6, ECO:0000250|UniProtKB:Q9EQE1, ECO:0000269|PubMed:11896061, ECO:0000269|PubMed:12192048, ECO:0000269|PubMed:20194620, ECO:0000269|PubMed:21965678}.
• Pathway: RNA transport - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Wnt Signaling Pathway;SUMO is proteolytically processed;Post-translational protein modification;Metabolism of proteins;Processing and activation of SUMO;SUMOylation (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.263
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.411
• hipred: Y
• hipred_score: 0.771
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.908

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Senp2
• Phenotype: homeostasis/metabolism phenotype; embryo phenotype; 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); 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: positive regulation of protein phosphorylation;heart development;dorsal/ventral axis specification;protein transport;Wnt signaling pathway;protein sumoylation;protein desumoylation;regulation of Wnt signaling pathway;negative regulation of protein ubiquitination;positive regulation of protein ubiquitination;protein destabilization;negative regulation of protein binding;regulation of DNA endoreduplication;negative regulation of chromatin binding;fat cell differentiation;positive regulation of transcription by RNA polymerase II;mRNA transport;trophoblast giant cell differentiation;labyrinthine layer development;spongiotrophoblast layer development;regulation of G1/S transition of mitotic cell cycle
• Cellular component: nucleus;nuclear pore;nucleoplasm;cytosol;PML body;nuclear membrane
• Molecular function: protein binding;protein domain specific binding;SUMO-specific endopeptidase activity;SUMO-specific isopeptidase activity