SENP7

SUMO specific peptidase 7, the group of SUMO specific peptidases

Basic information

Region (hg38): 3:101324205-101513241

Links

ENSG00000138468 ∙ NCBI:57337 ∙ OMIM:612846 ∙ HGNC:30402 ∙ Uniprot:Q9BQF6 ∙ 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 SENP7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SENP7 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			57	9	4	70
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	1	57	9	5

Variants in SENP7

This is a list of pathogenic ClinVar variants found in the SENP7 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-101325991-C-A		not specified	Uncertain significance (May 23, 2023)
3-101326008-G-A		Arthrogryposis multiplex congenita	Uncertain significance (Aug 01, 2024)
3-101326018-T-C		not specified	Uncertain significance (Jun 12, 2023)
3-101326029-G-A		not specified	Uncertain significance (Aug 13, 2021)
3-101327724-T-C		not specified	Uncertain significance (Dec 20, 2023)
3-101328508-G-C		not specified	Uncertain significance (May 15, 2024)
3-101328523-G-A		not specified	Uncertain significance (Dec 18, 2023)
3-101328672-C-T		not specified	Uncertain significance (Jun 24, 2022)
3-101330365-G-A		not specified	Uncertain significance (Mar 30, 2024)
3-101330374-C-T		not specified	Likely benign (Aug 12, 2021)
3-101330375-G-A		not specified	Uncertain significance (Feb 17, 2023)
3-101331990-G-A		not specified	Uncertain significance (Sep 13, 2023)
3-101332000-C-T		not specified	Uncertain significance (Oct 12, 2024)
3-101332041-T-C		not specified	Uncertain significance (Apr 15, 2024)
3-101332109-C-T		not specified	Likely benign (Aug 27, 2024)
3-101332803-T-C		not specified	Uncertain significance (Jan 20, 2023)
3-101337623-A-G		not specified	Uncertain significance (Apr 07, 2022)
3-101340102-A-G		not specified	Uncertain significance (Oct 20, 2021)
3-101341662-T-C		not specified	Uncertain significance (Feb 07, 2023)
3-101341664-T-A		not specified	Uncertain significance (Mar 30, 2022)
3-101341719-A-G		not specified	Uncertain significance (Dec 13, 2022)
3-101341763-G-A		not specified	Uncertain significance (Sep 27, 2024)
3-101341769-G-A		not specified	Likely benign (Jun 09, 2022)
3-101343688-G-T		not specified	Uncertain significance (Dec 14, 2021)
3-101343727-C-T		not specified	Uncertain significance (Mar 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SENP7	protein_coding	protein_coding	ENST00000394095	24	189037

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0733	0.927	125725	0	22	125747	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	382	518	0.738	0.0000259	6881
Missense in Polyphen		80	169.47	0.47205		2294
Synonymous	1.76	158	189	0.837	0.00000956	1918
Loss of Function	5.45	15	60.9	0.246	0.00000340	773

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000277	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000560	0.0000544
Finnish	0.000232	0.000231
European (Non-Finnish)	0.0000815	0.0000791
Middle Eastern	0.0000560	0.0000544
South Asian	0.0000770	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protease that deconjugates SUMO2 and SUMO3 from targeted proteins, but not SUMO1. Catalyzes the deconjugation of poly-SUMO2 and poly-SUMO3 chains. Has very low efficiency in processing full- length SUMO proteins to their mature forms. {ECO:0000269|PubMed:18799455}.

Recessive Scores

• pRec: 0.0847

Intolerance Scores

• loftool: 0.678
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.61

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.281
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.140

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Senp7
• Phenotype: pigmentation 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)

Gene ontology

• Biological process: protein desumoylation
• Cellular component: nucleus;cytoplasm
• Molecular function: protein binding;SUMO-specific endopeptidase activity