SENP6

SUMO specific peptidase 6, the group of SUMO specific peptidases

Basic information

Region (hg38): 6:75601508-75718281

Links

ENSG00000112701 ∙ NCBI:26054 ∙ OMIM:605003 ∙ HGNC:20944 ∙ Uniprot:Q9GZR1 ∙ 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 SENP6 gene.

• Inborn genetic diseases (31 variants)
• not provided (6 variants)
• Epicanthus;Delayed speech and language development;Synophrys;High, narrow palate (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SENP6 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				2	2	4
missense			30	2		32
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	30	5	2

Variants in SENP6

This is a list of pathogenic ClinVar variants found in the SENP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-75602535-G-C		not specified	Uncertain significance (Jun 06, 2023)
6-75602550-G-T		not specified	Uncertain significance (Aug 02, 2023)
6-75621576-A-T		not specified	Uncertain significance (Oct 03, 2023)
6-75621592-A-G			Uncertain significance (Aug 07, 2018)
6-75621621-A-C		not specified	Uncertain significance (Oct 02, 2023)
6-75633591-G-A		not specified	Likely benign (Nov 30, 2021)
6-75633644-A-G		not specified	Uncertain significance (Apr 25, 2022)
6-75633714-A-G		not specified	Uncertain significance (Mar 22, 2022)
6-75634787-C-G		not specified	Uncertain significance (Sep 14, 2022)
6-75640694-C-T		Epicanthus;Delayed speech and language development;Synophrys;High, narrow palate	Likely benign (-)
6-75640695-G-A		not specified	Likely benign (Dec 20, 2023)
6-75647742-C-T		not specified	Uncertain significance (Dec 09, 2023)
6-75647772-C-T		not specified	Uncertain significance (May 27, 2022)
6-75647788-G-T			Benign (Apr 16, 2018)
6-75659352-A-G		not specified	Uncertain significance (Jan 06, 2023)
6-75663286-G-A			Benign (Apr 16, 2018)
6-75663303-C-T		not specified	Uncertain significance (Feb 28, 2023)
6-75663327-C-A		not specified	Uncertain significance (Jan 26, 2023)
6-75663444-T-C		not specified	Uncertain significance (Aug 16, 2022)
6-75666723-A-G		not specified	Uncertain significance (Apr 05, 2023)
6-75666865-G-A		not specified	Likely benign (Feb 27, 2024)
6-75670617-A-T		not specified	Uncertain significance (Jan 23, 2023)
6-75670706-A-G		not specified	Uncertain significance (Apr 18, 2023)
6-75675867-C-A		not specified	Likely benign (Jul 14, 2023)
6-75675871-G-T		not specified	Uncertain significance (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SENP6	protein_coding	protein_coding	ENST00000447266	24	116773

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000207	124762	0	18	124780	0.0000721

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.999	500	567	0.882	0.0000288	7386
Missense in Polyphen		154	221.48	0.69531		2935
Synonymous	0.0423	190	191	0.996	0.00000962	1966
Loss of Function	6.42	7	61.3	0.114	0.00000370	749

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.000225	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.0000990	0.0000971
Middle Eastern	0.000225	0.000223
South Asian	0.0000655	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protease that deconjugates SUMO1, SUMO2 and SUMO3 from targeted proteins. Processes preferentially poly-SUMO2 and poly- SUMO3 chains, but does not efficiently process SUMO1, SUMO2 and SUMO3 precursors. Deconjugates SUMO1 from RXRA, leading to transcriptional activation. Involved in chromosome alignment and spindle assembly, by regulating the kinetochore CENPH-CENPI-CENPK complex. Desumoylates PML and CENPI, protecting them from degradation by the ubiquitin ligase RNF4, which targets polysumoylated proteins for proteasomal degradation. Desumoylates also RPA1, thus preventing recruitment of RAD51 to the DNA damage foci to initiate DNA repair through homologous recombination. {ECO:0000269|PubMed:16912044, ECO:0000269|PubMed:17000875, ECO:0000269|PubMed:18799455, ECO:0000269|PubMed:20212317, ECO:0000269|PubMed:20705237, ECO:0000269|PubMed:21148299}.

Recessive Scores

• pRec: 0.0827

Intolerance Scores

• loftool: 0.558
• rvis_EVS: 0.36
• rvis_percentile_EVS: 74.68

Haploinsufficiency Scores

• pHI: 0.705
• hipred: Y
• hipred_score: 0.704
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.902

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Senp6
• 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)

Gene ontology

• Biological process: protein sumoylation;protein desumoylation;protein modification by small protein removal;regulation of spindle assembly;regulation of kinetochore assembly
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol
• Molecular function: protein binding;SUMO-specific endopeptidase activity