SUMO4

small ubiquitin like modifier 4

Basic information

Region (hg38): 6:149400262-149401278

Previous symbols: [ "SMT3H4", "IDDM5" ]

Links

ENSG00000177688 ∙ NCBI:387082 ∙ OMIM:608829 ∙ HGNC:21181 ∙ Uniprot:Q6EEV6 ∙ 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 SUMO4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUMO4 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			6	2	1	9
nonsense						0
start loss				2		2
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	5	1

Variants in SUMO4

This is a list of pathogenic ClinVar variants found in the SUMO4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-149400392-A-G			Likely benign (Feb 15, 2022)
6-149400393-T-C			Likely benign (Feb 01, 2023)
6-149400418-A-C		not specified	Uncertain significance (Mar 14, 2023)
6-149400490-G-T		not specified	Uncertain significance (May 17, 2023)
6-149400493-T-G		not specified	Uncertain significance (Dec 26, 2023)
6-149400543-G-A			Likely benign (Feb 08, 2018)
6-149400554-G-A		Type 1 diabetes mellitus 5 • not specified	Benign (May 04, 2022)
6-149400559-G-A			Likely benign (Mar 01, 2024)
6-149400585-A-G		not specified	Uncertain significance (Dec 09, 2024)
6-149400590-A-G		not specified	Uncertain significance (Jan 19, 2022)
6-149400597-G-C		not specified	Uncertain significance (Feb 21, 2024)
6-149400605-A-G		not specified	Uncertain significance (May 06, 2022)
6-149400663-C-T			Likely benign (Feb 08, 2018)
6-149400675-A-G		not specified	Uncertain significance (Oct 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUMO4	protein_coding	protein_coding	ENST00000326669	1	683

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.164	48	51.3	0.935	0.00000260	624
Missense in Polyphen		4	4.6475	0.86068		83
Synonymous	-0.218	21	19.8	1.06	0.00000113	178
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ubiquitin-like protein which can be covalently attached to target lysines as a monomer. Does not seem to be involved in protein degradation and may modulate protein subcellular localization, stability or activity. Upon oxidative stress, conjugates to various anti-oxidant enzymes, chaperones, and stress defense proteins. May also conjugate to NFKBIA, TFAP2A and FOS, negatively regulating their transcriptional activity, and to NR3C1, positively regulating its transcriptional activity. Covalent attachment to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I. {ECO:0000269|PubMed:15123604, ECO:0000269|PubMed:15247916, ECO:0000269|PubMed:16236267}.
• Disease: DISEASE: Diabetes mellitus, insulin-dependent, 5 (IDDM5) [MIM:600320]: A form of diabetes mellitus, a multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical features are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269|PubMed:15678134, ECO:0000269|PubMed:15678135, ECO:0000269|PubMed:15678137}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.
• Pathway: RNA transport - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.151

Intolerance Scores

• loftool: 0.722
• rvis_EVS: 0.88
• rvis_percentile_EVS: 88.96

Haploinsufficiency Scores

• pHI: 0.216
• hipred: N
• hipred_score: 0.254
• ghis: 0.405

Essentials

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

Gene Damage Prediction

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

Gene ontology

• Biological process: protein sumoylation
• Cellular component: nucleus
• Molecular function: protein tag;ubiquitin-like protein ligase binding