SENP3

SUMO specific peptidase 3, the group of Large ribosomal subunit biogenesis complex|SUMO specific peptidases

Basic information

Region (hg38): 17:7561918-7571969

Links

ENSG00000161956 ∙ NCBI:26168 ∙ OMIM:612844 ∙ HGNC:17862 ∙ Uniprot:Q9H4L4 ∙ 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 SENP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SENP3 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in SENP3

This is a list of pathogenic ClinVar variants found in the SENP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7563155-C-G		not specified	Uncertain significance (Jan 16, 2024)
17-7563167-C-T		not specified	Uncertain significance (Dec 03, 2021)
17-7563305-G-A		not specified	Uncertain significance (Apr 28, 2023)
17-7563331-G-C		not specified	Uncertain significance (May 30, 2023)
17-7563338-G-A		not specified	Uncertain significance (Sep 29, 2023)
17-7563377-A-G		not specified	Uncertain significance (Aug 02, 2021)
17-7563430-T-A		not specified	Uncertain significance (May 31, 2022)
17-7563485-C-T		not specified	Uncertain significance (Jun 22, 2021)
17-7563546-G-A		not specified	Uncertain significance (Apr 25, 2022)
17-7563614-C-T		not specified	Uncertain significance (Jun 22, 2024)
17-7563635-G-C		not specified	Uncertain significance (Feb 23, 2023)
17-7563704-A-G		not specified	Uncertain significance (Dec 04, 2023)
17-7563731-C-T		not specified	Uncertain significance (Sep 16, 2021)
17-7563746-G-T		not specified	Uncertain significance (Mar 01, 2024)
17-7563762-C-T		not specified	Uncertain significance (Dec 06, 2021)
17-7563788-T-G		not specified	Uncertain significance (Jun 10, 2024)
17-7564625-G-A		not specified	Uncertain significance (Mar 01, 2024)
17-7564651-G-C		not specified	Uncertain significance (Dec 14, 2022)
17-7564681-G-C		not specified	Uncertain significance (Jul 26, 2022)
17-7564696-C-A		not specified	Uncertain significance (May 27, 2022)
17-7564697-C-T		not specified	Uncertain significance (May 14, 2024)
17-7564727-T-C		not specified	Uncertain significance (Dec 27, 2022)
17-7564737-C-T		not specified	Likely benign (Jan 02, 2024)
17-7564817-C-T		not specified	Uncertain significance (Oct 02, 2023)
17-7564819-G-A		not specified	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SENP3	protein_coding	protein_coding	ENST00000429205	11	10096

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.848	0.152	124629	0	4	124633	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.56	204	336	0.607	0.0000199	3676
Missense in Polyphen		32	85.231	0.37545		981
Synonymous	0.298	120	124	0.966	0.00000658	1157
Loss of Function	4.32	6	32.6	0.184	0.00000213	311

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000583	0.0000583
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000896	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protease that releases SUMO2 and SUMO3 monomers from sumoylated substrates, but has only weak activity against SUMO1 conjugates. Deconjugates SUMO2 from MEF2D, which increases its transcriptional activation capability. Deconjugates SUMO2 and SUMO3 from CDCA8. Redox sensor that, when redistributed into nucleoplasm, can act as an effector to enhance HIF1A transcriptional activity by desumoylating EP300. Required for rRNA processing through deconjugation of SUMO2 and SUMO3 from nucleophosmin, NPM1. Plays a role in the regulation of sumoylation status of ZNF148. Functions as a component of the Five Friends of Methylated CHTOP (5FMC) complex; the 5FMC complex is recruited to ZNF148 by methylated CHTOP, leading to desumoylation of ZNF148 and subsequent transactivation of ZNF148 target genes. {ECO:0000269|PubMed:15743823, ECO:0000269|PubMed:16608850, ECO:0000269|PubMed:18259216, ECO:0000269|PubMed:18946085, ECO:0000269|PubMed:19015314, ECO:0000269|PubMed:19680224, ECO:0000269|PubMed:22872859}.

Recessive Scores

• pRec: 0.109

Haploinsufficiency Scores

• pHI: 0.733
• hipred: Y
• hipred_score: 0.774
• ghis: 0.688

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.983

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Senp3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: rRNA processing;protein desumoylation
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;MLL1 complex
• Molecular function: protein binding;cysteine-type peptidase activity