SUMO1

Chr 2Isolated cases

small ubiquitin like modifier 1

Also known as: DAP1, GMP1, OFC10, PIC1, SENP2, SMT3, SMT3C, SMT3H3

NCBI Gene: 7341ENSG00000116030UniProt: P63165

This gene encodes a protein that is a member of the SUMO (small ubiquitin-like modifier) protein family. It functions in a manner similar to ubiquitin in that it is bound to target proteins as part of a post-translational modification system. However, unlike ubiquitin which targets proteins for degradation, this protein is involved in a variety of cellular processes, such as nuclear transport, transcriptional regulation, apoptosis, and protein stability. It is not active until the last four amino acids of the carboxy-terminus have been cleaved off. Several pseudogenes have been reported for this gene. Alternate transcriptional splice variants encoding different isoforms have been characterized. [provided by RefSeq, Jul 2008]

Primary Disease Associations & Inheritance

?Orofacial cleft 10MIM #613705
Isolated cases
UniProtNon-syndromic orofacial cleft 10
54
ClinVar variants
30
Pathogenic / LP
0.86
pLI score
0
Active trials
Clinical Summary— SUMO1
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.86) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
30 Pathogenic / Likely Pathogenic· 18 VUS of 54 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.46LOEUF
pLI 0.861
Z-score 2.36
OE 0.00 (0.00–0.46)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.51Z-score
OE missense 0.38 (0.26–0.57)
18 obs / 47.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.00 (0.00–0.46)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.38 (0.26–0.57)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.06
0≤1.21.6
LoF obs/exp: 0 / 6.5Missense obs/exp: 18 / 47.1Syn Z: -0.19

ClinVar Variant Classifications

54 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic29
Likely Pathogenic1
VUS18
Likely Benign2
Benign4
29
Pathogenic
1
Likely Pathogenic
18
VUS
2
Likely Benign
4
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
29
0
29
Likely Pathogenic
0
0
1
0
1
VUS
0
2
16
0
18
Likely Benign
0
0
2
0
2
Benign
0
0
4
0
4
Total0252054

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SUMO1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

SUMO1-related cleft lip with or without cleft palate

limited
ADLoss Of FunctionAbsent Gene Product
Dev. Disorders
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

?Orofacial cleft 10

MIM #613705

Molecular basis of disorder known

Isolated cases
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
A Comprehensive Overview on Myositis-Specific Antibodies: New and Old Biomarkers in Idiopathic Inflammatory Myopathy.
Satoh M et al.·Clin Rev Allergy Immunol
2017Review
GTPBP4 promotes hepatocellular carcinoma progression and metastasis via the PKM2 dependent glucose metabolism.
Zhou Q et al.·Redox Biol
2022
Paralogue-Specific Roles of SUMO1 and SUMO2/3 in Protein Quality Control and Associated Diseases.
Wang W et al.·Cells
2023Review
Dynamic SUMOylation of MORC2 orchestrates chromatin remodelling and DNA repair in response to DNA damage and drives chemoresistance in breast cancer.
Zhang FL et al.·Theranostics
2023Functional
Decitabine cytotoxicity is promoted by dCMP deaminase DCTD and mitigated by SUMO-dependent E3 ligase TOPORS.
Carnie CJ et al.·EMBO J
2024
ROS-mediated up-regulation of SAE1 by Helicobacter pylori promotes human gastric tumor genesis and progression.
Shi L et al.·J Transl Med
2024
Sumoylation in Craniofacial Disorders.
Pauws E et al.·Adv Exp Med Biol
2017Review
SUMOylation of annexin A6 retards cell migration and tumor growth by suppressing RHOU/AKT1-involved EMT in hepatocellular carcinoma.
Yang Y et al.·Cell Commun Signal
2024
SUMO-regulated mitochondrial function in Parkinson's disease.
Guerra de Souza AC et al.·J Neurochem
2016Review
Ginkgolic acid inhibits the expression of SAE1 and induces ferroptosis to exert an anti-hepatic fibrosis effect.
Zhang S et al.·Phytomedicine
2024
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
A TFAP4-UBC9-SUMO1 axis orchestrates pathological mitochondrial hyperfission in diabetic complications.
Jin Z et al.·Acta Diabetol
2026
Suoquan Yishen formula attenuates ectopic lipid deposition in diabetic kidney disease by inhibiting UBC9-mediated SUMO1 modification of DRP1.
Wang J et al.·J Ethnopharmacol
2026
Biomolecular Correlates of Chronic Affective Dysregulation in PTSD: A Combined Assessment Using the Cornell Dysthymia Rating Scale (CDRS) and the Serum Markers SUMO1, MDA, CX3CL1, and UCHL1.
Woźny-Rasała I et al.·Int J Mol Sci
2025🔓 Open Access
SUMO1 promotes malignancy and chemoresistance in colorectal cancer: Clinical and functional evidence.
Xu A et al.·Tissue Cell
2026Functional
Chenodeoxycholic Acid Alleviates High-Fat Diet-Induced Lipid Deposition via FXR/SHP/PIAS1/SUMO1-Dependent SREBP1K264 SUMOylation in Yellow Catfish.
Zheng H et al.·J Nutr
2025
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools