SUMO4 (small ubiquitin like modifier 4) - Rat Genome Database

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Gene: SUMO4 (small ubiquitin like modifier 4) Homo sapiens
Analyze
Symbol: SUMO4
Name: small ubiquitin like modifier 4
RGD ID: 1349888
HGNC Page HGNC:21181
Description: Predicted to enable protein tag activity and ubiquitin-like protein ligase binding activity. Involved in several processes, including protein sumoylation; regulation of canonical NF-kappaB signal transduction; and regulation of protein localization to nucleus. Part of SUMO ligase complex. Implicated in type 1 diabetes mellitus 5.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: dJ281H8.4; IDDM5; insulin-dependent diabetes mellitus 5; small ubiquitin-like modifier 4; small ubiquitin-like modifier 4 protein; small ubiquitin-related modifier 4; SMT3 suppressor of mif two 3 homolog 2; SMT3 suppressor of mif two 3 homolog 4; smt3 suppressor of mif two 3 homolog 4 (yeast); SMT3H4; SUMO-4
RGD Orthologs
Rat
Bonobo
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386149,400,262 - 149,401,278 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6149,400,262 - 149,401,278 (+)EnsemblGRCh38hg38GRCh38
GRCh376149,721,398 - 149,722,414 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366149,763,188 - 149,763,875 (+)NCBINCBI36Build 36hg18NCBI36
Build 346149,763,187 - 149,763,873NCBI
Celera6150,456,593 - 150,457,280 (+)NCBICelera
Cytogenetic Map6q25.1NCBI
HuRef6147,288,256 - 147,288,943 (+)NCBIHuRef
CHM1_16149,986,244 - 149,986,931 (+)NCBICHM1_1
T2T-CHM13v2.06150,600,139 - 150,601,155 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,IEA)
SUMO ligase complex  (IDA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8072542   PMID:8733139   PMID:12477932   PMID:12901503   PMID:14574404   PMID:15123604   PMID:15247916   PMID:15678134   PMID:15678135   PMID:15678137   PMID:15730420   PMID:16159953  
PMID:16198310   PMID:16236267   PMID:16249223   PMID:16306380   PMID:16735488   PMID:16755651   PMID:16821265   PMID:17130530   PMID:17130532   PMID:17130563   PMID:17130565   PMID:17229939  
PMID:17373940   PMID:17374705   PMID:17452059   PMID:17459725   PMID:17554341   PMID:17558709   PMID:17660269   PMID:17926234   PMID:17990297   PMID:18330586   PMID:18466472   PMID:18466531  
PMID:18657476   PMID:18708028   PMID:19122825   PMID:19222990   PMID:19410319   PMID:19915388   PMID:19956095   PMID:20448286   PMID:20518843   PMID:20728233   PMID:20868570   PMID:21158221  
PMID:21671169   PMID:21873635   PMID:21901353   PMID:21906435   PMID:22425950   PMID:22884980   PMID:22936652   PMID:23042402   PMID:25189908   PMID:25281560   PMID:25921289   PMID:26344197  
PMID:27055882   PMID:28494838   PMID:28545138   PMID:28689037   PMID:28941036   PMID:29459360   PMID:31527615   PMID:32237992   PMID:32694731   PMID:33729478   PMID:35256949   PMID:35503374  
PMID:35987950   PMID:36964488   PMID:37066695  


Genomics

Comparative Map Data
SUMO4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386149,400,262 - 149,401,278 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6149,400,262 - 149,401,278 (+)EnsemblGRCh38hg38GRCh38
GRCh376149,721,398 - 149,722,414 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366149,763,188 - 149,763,875 (+)NCBINCBI36Build 36hg18NCBI36
Build 346149,763,187 - 149,763,873NCBI
Celera6150,456,593 - 150,457,280 (+)NCBICelera
Cytogenetic Map6q25.1NCBI
HuRef6147,288,256 - 147,288,943 (+)NCBIHuRef
CHM1_16149,986,244 - 149,986,931 (+)NCBICHM1_1
T2T-CHM13v2.06150,600,139 - 150,601,155 (+)NCBIT2T-CHM13v2.0
LOC120095693
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81192,667,392 - 92,668,480 (+)NCBIGRCr8
mRatBN7.21179,163,457 - 79,164,088 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1179,163,634 - 79,163,960 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0 Ensembl1182,813,691 - 82,814,017 (+)NCBIRnor6.0rn6Rnor6.0
Cytogenetic Map11q23NCBI
SUMO4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25169,426,809 - 169,433,107 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16167,320,438 - 167,321,470 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06147,219,279 - 147,221,125 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16151,925,637 - 151,926,346 (+)NCBIpanpan1.1PanPan1.1panPan2

Variants

.
Variants in SUMO4
9 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001002255.2(SUMO4):c.163G>A (p.Val55Met) single nucleotide variant Type 1 diabetes mellitus 5 [RCV000002143]|not provided [RCV001668122]|not specified [RCV002247237] Chr6:149400554 [GRCh38]
Chr6:149721690 [GRCh37]
Chr6:6q25.1		 pathogenic|risk factor|benign
GRCh38/hg38 6q24.1-27(chr6:141132990-169339571)x3 copy number gain See cases [RCV000050604] Chr6:141132990..169339571 [GRCh38]
Chr6:141454127..169739666 [GRCh37]
Chr6:141495820..169481591 [NCBI36]
Chr6:6q24.1-27		 pathogenic
GRCh38/hg38 6q24.3-25.1(chr6:146481119-151427629)x1 copy number loss See cases [RCV000051005] Chr6:146481119..151427629 [GRCh38]
Chr6:146802255..151748764 [GRCh37]
Chr6:146843948..151790457 [NCBI36]
Chr6:6q24.3-25.1		 pathogenic
GRCh38/hg38 6q24.2-25.2(chr6:144932561-152985364)x1 copy number loss See cases [RCV000052206] Chr6:144932561..152985364 [GRCh38]
Chr6:145253697..153306499 [GRCh37]
Chr6:145295390..153348192 [NCBI36]
Chr6:6q24.2-25.2		 pathogenic
GRCh38/hg38 6q24.3-25.1(chr6:147805119-150893715)x1 copy number loss See cases [RCV000135408] Chr6:147805119..150893715 [GRCh38]
Chr6:148126255..151214851 [GRCh37]
Chr6:148167948..151256544 [NCBI36]
Chr6:6q24.3-25.1		 pathogenic
GRCh38/hg38 6q25.1(chr6:149333404-149527861)x3 copy number gain See cases [RCV000135603] Chr6:149333404..149527861 [GRCh38]
Chr6:149654540..149848997 [GRCh37]
Chr6:149696233..149890690 [NCBI36]
Chr6:6q25.1		 pathogenic|uncertain significance
GRCh38/hg38 6q24.3-25.1(chr6:148112335-149649984)x1 copy number loss See cases [RCV000136969] Chr6:148112335..149649984 [GRCh38]
Chr6:148433471..149971120 [GRCh37]
Chr6:148475164..150012813 [NCBI36]
Chr6:6q24.3-25.1		 pathogenic
GRCh38/hg38 6q23.3-25.3(chr6:135358150-155455117)x3 copy number gain See cases [RCV000136826] Chr6:135358150..155455117 [GRCh38]
Chr6:135679288..155776251 [GRCh37]
Chr6:135720981..155817943 [NCBI36]
Chr6:6q23.3-25.3		 pathogenic
GRCh38/hg38 6q24.3-25.1(chr6:147580351-150227963)x3 copy number gain See cases [RCV000138362] Chr6:147580351..150227963 [GRCh38]
Chr6:147901487..150549099 [GRCh37]
Chr6:147943180..150590792 [NCBI36]
Chr6:6q24.3-25.1		 uncertain significance
GRCh38/hg38 6q25.1(chr6:149056723-149435037)x1 copy number loss See cases [RCV000141698] Chr6:149056723..149435037 [GRCh38]
Chr6:149377859..149756173 [GRCh37]
Chr6:149419552..149797866 [NCBI36]
Chr6:6q25.1		 uncertain significance
GRCh38/hg38 6q23.2-27(chr6:133537271-165875545)x3 copy number gain See cases [RCV000143444] Chr6:133537271..165875545 [GRCh38]
Chr6:133858409..166289033 [GRCh37]
Chr6:133900102..166209023 [NCBI36]
Chr6:6q23.2-27		 pathogenic
GRCh37/hg19 6q24.2-25.1(chr6:144075695-152337005)x1 copy number loss See cases [RCV000448815] Chr6:144075695..152337005 [GRCh37]
Chr6:6q24.2-25.1		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)x3 copy number gain See cases [RCV000512067] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482) copy number gain See cases [RCV000510595] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6q24.3-25.1(chr6:148364229-149928368)x1 copy number loss See cases [RCV000511918] Chr6:148364229..149928368 [GRCh37]
Chr6:6q24.3-25.1		 likely pathogenic
GRCh37/hg19 6q24.1-25.1(chr6:139513020-150389231)x1 copy number loss See cases [RCV000510942] Chr6:139513020..150389231 [GRCh37]
Chr6:6q24.1-25.1		 pathogenic
NM_001002255.2(SUMO4):c.99G>T (p.Lys33Asn) single nucleotide variant Inborn genetic diseases [RCV003251438] Chr6:149400490 [GRCh38]
Chr6:149721626 [GRCh37]
Chr6:6q25.1		 uncertain significance
GRCh37/hg19 6q24.2-25.1(chr6:144947731-150266155)x1 copy number loss not provided [RCV000682729] Chr6:144947731..150266155 [GRCh37]
Chr6:6q24.2-25.1		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:60107-171054786)x3 copy number gain not provided [RCV000745400] Chr6:60107..171054786 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:165632-170919470)x3 copy number gain not provided [RCV000745404] Chr6:165632..170919470 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:108666-170980171)x3 copy number gain not provided [RCV000745403] Chr6:108666..170980171 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6q24.3-25.1(chr6:148690764-150494873)x1 copy number loss See cases [RCV000790589] Chr6:148690764..150494873 [GRCh37]
Chr6:6q24.3-25.1		 pathogenic
GRCh37/hg19 6q25.1-25.2(chr6:149431322-154120064)x1 copy number loss not provided [RCV001005856] Chr6:149431322..154120064 [GRCh37]
Chr6:6q25.1-25.2		 pathogenic
GRCh37/hg19 6q24.3-25.3(chr6:148195086-160127254)x3 copy number gain not provided [RCV000846496] Chr6:148195086..160127254 [GRCh37]
Chr6:6q24.3-25.3		 pathogenic
GRCh37/hg19 6q25.1(chr6:149478703-149814558)x3 copy number gain not provided [RCV000845958] Chr6:149478703..149814558 [GRCh37]
Chr6:6q25.1		 uncertain significance
NM_001002255.2(SUMO4):c.152G>A (p.Arg51Gln) single nucleotide variant not provided [RCV000956427] Chr6:149400543 [GRCh38]
Chr6:149721679 [GRCh37]
Chr6:6q25.1		 likely benign
NM_001002255.2(SUMO4):c.272C>T (p.Thr91Met) single nucleotide variant not provided [RCV000956428] Chr6:149400663 [GRCh38]
Chr6:149721799 [GRCh37]
Chr6:6q25.1		 likely benign
NC_000006.11:g.(?_149691134)_(149730855_?)del deletion not provided [RCV001951605] Chr6:149691134..149730855 [GRCh37]
Chr6:6q25.1		 pathogenic
NM_001002255.2(SUMO4):c.1A>G (p.Met1Val) single nucleotide variant not provided [RCV002275823] Chr6:149400392 [GRCh38]
Chr6:149721528 [GRCh37]
Chr6:6q25.1		 likely benign
NM_001002255.2(SUMO4):c.214A>G (p.Lys72Glu) single nucleotide variant Inborn genetic diseases [RCV002832133] Chr6:149400605 [GRCh38]
Chr6:149721741 [GRCh37]
Chr6:6q25.1		 uncertain significance
NM_001002255.2(SUMO4):c.199A>G (p.Ile67Val) single nucleotide variant Inborn genetic diseases [RCV003010818] Chr6:149400590 [GRCh38]
Chr6:149721726 [GRCh37]
Chr6:6q25.1		 uncertain significance
NM_001002255.2(SUMO4):c.27A>C (p.Glu9Asp) single nucleotide variant Inborn genetic diseases [RCV003202088] Chr6:149400418 [GRCh38]
Chr6:149721554 [GRCh37]
Chr6:6q25.1		 uncertain significance
NM_001002255.2(SUMO4):c.2T>C (p.Met1Thr) single nucleotide variant not provided [RCV003428981] Chr6:149400393 [GRCh38]
Chr6:149721529 [GRCh37]
Chr6:6q25.1		 likely benign
GRCh37/hg19 6q22.31-25.3(chr6:119840686-156623091)x3 copy number gain not specified [RCV003986631] Chr6:119840686..156623091 [GRCh37]
Chr6:6q22.31-25.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:133
Count of miRNA genes:128
Interacting mature miRNAs:129
Transcripts:ENST00000326669
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region
D6S441  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376153,814,301 - 153,814,466UniSTSGRCh37
Build 366153,855,994 - 153,856,159RGDNCBI36
Celera6154,548,742 - 154,548,909RGD
Cytogenetic Map6q25UniSTS
HuRef6151,377,615 - 151,377,782UniSTS
Marshfield Genetic Map6154.1RGD
Marshfield Genetic Map6154.1UniSTS
Genethon Genetic Map6155.3UniSTS
Whitehead-RH Map6816.5UniSTS
Whitehead-YAC Contig Map6 UniSTS
NCBI RH Map61610.7UniSTS
D6S264  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376166,709,199 - 166,709,370UniSTSGRCh37
GRCh376166,709,250 - 166,709,371UniSTSGRCh37
Build 366166,629,240 - 166,629,361RGDNCBI36
Celera6167,448,614 - 167,448,725RGD
Celera6167,448,563 - 167,448,724UniSTS
HuRef6164,180,198 - 164,180,305UniSTS
HuRef6164,180,147 - 164,180,304UniSTS
Marshfield Genetic Map6179.07RGD
Genethon Genetic Map6179.1UniSTS
Stanford-G3 RH Map66515.0UniSTS
GeneMap99-GB4 RH Map6638.5UniSTS
GeneMap99-G3 RH Map66818.0UniSTS
D6S264  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map6q25UniSTS
Marshfield Genetic Map6179.07UniSTS
Genethon Genetic Map6179.1UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 6 4 12 1 1 1 4 1 1
Low 984 1253 1191 400 979 292 1851 538 1428 166 1129 1073 114 617 1145 4
Below cutoff 1323 1549 490 204 759 155 2204 1454 2084 206 269 480 55 531 1447

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000326669   ⟹   ENSP00000318635
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl6149,400,262 - 149,401,278 (+)Ensembl
RefSeq Acc Id: NM_001002255   ⟹   NP_001002255
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh386149,400,262 - 149,401,278 (+)NCBI
GRCh376149,721,284 - 149,722,182 (+)NCBI
Build 366149,763,188 - 149,763,875 (+)NCBI Archive
HuRef6147,288,256 - 147,288,943 (+)ENTREZGENE
CHM1_16149,986,244 - 149,986,931 (+)NCBI
T2T-CHM13v2.06150,600,139 - 150,601,155 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001002255 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI30306 (Get FASTA)   NCBI Sequence Viewer  
  AAR04484 (Get FASTA)   NCBI Sequence Viewer  
  BAH05006 (Get FASTA)   NCBI Sequence Viewer  
  EAW47808 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000318635
  ENSP00000318635.4
GenBank Protein Q6EEV6 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001002255   ⟸   NM_001002255
- UniProtKB: A1L3W5 (UniProtKB/Swiss-Prot),   Q6EEV6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000318635   ⟸   ENST00000326669
Protein Domains
Ubiquitin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6EEV6-F1-model_v2 AlphaFold Q6EEV6 1-95 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:21181 AgrOrtholog
COSMIC SUMO4 COSMIC
Ensembl Genes ENSG00000177688 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000326669 ENTREZGENE
  ENST00000326669.6 UniProtKB/Swiss-Prot
GTEx ENSG00000177688 GTEx
HGNC ID HGNC:21181 ENTREZGENE
Human Proteome Map SUMO4 Human Proteome Map
InterPro Rad60/SUMO-like_dom UniProtKB/Swiss-Prot
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot
  Ubiquitin_dom UniProtKB/Swiss-Prot
KEGG Report hsa:387082 UniProtKB/Swiss-Prot
NCBI Gene 387082 ENTREZGENE
OMIM 608829 OMIM
PANTHER SMALL UBIQUITIN-RELATED MODIFIER UniProtKB/Swiss-Prot
  SMALL UBIQUITIN-RELATED MODIFIER 3-RELATED UniProtKB/Swiss-Prot
Pfam Rad60-SLD UniProtKB/Swiss-Prot
PharmGKB PA134979206 PharmGKB
PROSITE UBIQUITIN_2 UniProtKB/Swiss-Prot
SMART UBQ UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54236 UniProtKB/Swiss-Prot
UniProt A1L3W5 ENTREZGENE
  Q6EEV6 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A1L3W5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-02-19 SUMO4  small ubiquitin like modifier 4  SUMO4  small ubiquitin-like modifier 4  Symbol and/or name change 5135510 APPROVED
2016-04-05 SUMO4  small ubiquitin-like modifier 4  IDDM5  insulin-dependent diabetes mellitus 5  Data merged from RGD:1348820 737654 PROVISIONAL
2013-06-11 SUMO4  small ubiquitin-like modifier 4  SUMO4  SMT3 suppressor of mif two 3 homolog 4 (S. cerevisiae)  Symbol and/or name change 5135510 APPROVED