SUMO2

small ubiquitin like modifier 2

Basic information

Region (hg38): 17:75165585-75182959

Previous symbols: [ "SMT3H2" ]

Links

ENSG00000188612

∙ NCBI:6613 ∙ OMIM:603042 ∙ HGNC:11125 ∙ Uniprot:P61956 ∙ 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 SUMO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUMO2 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1 clinvar	1
Total	0	0	0	0	1

Variants in SUMO2

This is a list of pathogenic ClinVar variants found in the SUMO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-75182862-C-T			Benign (May 18, 2021)	1257423

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUMO2	protein_coding	protein_coding	ENST00000420826	4	15671

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.869	0.129	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.20	6	49.7	0.121	0.00000253	631
Missense in Polyphen		0	2.5838	0		45
Synonymous	-0.0721	19	18.6	1.02	0.00000114	159
Loss of Function	2.39	0	6.65	0.00	4.37e-7	70

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Function: FUNCTION: Ubiquitin-like protein that can be covalently attached to proteins as a monomer or as a lysine-linked polymer. Covalent attachment via an isopeptide bond to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, and can be promoted by an E3 ligase such as PIAS1-4, RANBP2, CBX4 or ZNF451 (PubMed:26524494). This post-translational modification on lysine residues of proteins plays a crucial role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Polymeric SUMO2 chains are also susceptible to polyubiquitination which functions as a signal for proteasomal degradation of modified proteins (PubMed:18408734, PubMed:18538659, PubMed:21965678, PubMed:9556629). Plays a role in the regulation of sumoylation status of SETX (PubMed:24105744). {ECO:0000269|PubMed:18408734, ECO:0000269|PubMed:18538659, ECO:0000269|PubMed:21965678, ECO:0000269|PubMed:24105744, ECO:0000269|PubMed:26524494, ECO:0000269|PubMed:9556629}.;
Pathway: RNA transport - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;DNA Double-Strand Break Repair;Metabolism of lipids;SUMO is conjugated to E1 (UBA2:SAE1);SUMO is transferred from E1 to E2 (UBE2I, UBC9);SUMO is proteolytically processed;SUMOylation of DNA damage response and repair proteins;SUMOylation of transcription factors;Homology Directed Repair;SUMOylation of chromatin organization proteins;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMOylation of DNA replication proteins;SUMO E3 ligases SUMOylate target proteins;basic mechanisms of sumoylation;Metabolism of proteins;Metabolism;Processing and activation of SUMO;Metabolism of steroids;SUMOylation;Vitamin D (calciferol) metabolism;Glucocorticoid receptor regulatory network;Formation of Incision Complex in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Processing of DNA double-strand break ends;Nucleotide Excision Repair;Steroid hormones (Consensus)

Intolerance Scores

loftool
rvis_EVS: 0.17
rvis_percentile_EVS: 65.04

Haploinsufficiency Scores

pHI
hipred: Y
hipred_score: 0.746
ghis: 0.632

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.914

Mouse Genome Informatics

Gene name: Sumo2
Phenotype: growth/size/body region phenotype; cellular 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); normal 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);

Gene ontology

Biological process: protein sumoylation;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;positive regulation of transcription by RNA polymerase II
Cellular component: nucleus;nucleoplasm;PML body
Molecular function: transcription corepressor binding;RNA binding;protein binding;SUMO transferase activity;protein tag;ubiquitin protein ligase binding;ubiquitin-like protein ligase binding