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GeneE
27 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SMC3
structural maintenance of chromosomes 3
Chromosome 10 Β· 10q25.2
NCBI Gene: 9126Ensembl: ENSG00000108055.12HGNC: HGNC:2468UniProt: Q9UQE7
298PubMed Papers
21Diseases
0Drugs
79Pathogenic Variants
FUNCTIONAL ROLE
DNA RepairHighly ConstrainedHub Gene
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
nucleoplasmmitotic spindle polecohesin complexmeiotic cohesin complexCornelia de Lange syndromegenetic disorderWiedemann-Steiner syndromecardiac arrest
✦AI Summary

SMC3 is a central structural component of the cohesin complex, a multisubunit ring that entraps sister chr10 during cell division 1. Beyond its canonical role in sister chr10 cohesion, SMC3 participates in DNA repair, spindle pole assembly, and gene regulation through chr10 looping 1. In response to DNA damage, the ATM-ESCO2-SMC3 axis functions critically: ATM phosphorylates acetyltransferase ESCO2, which then acetylates SMC3 to stabilize cohesin conformation, promote 53BP1 recruitment, and safeguard genome integrity 2. During normal mitosis, SMC3 acetylation must be precisely controlled through symmetric mechanisms involving GSK3-regulated ESCO2 dimerization to ensure cohesion establishes exclusively between nascent sister chr10 3. Pathogenic variants in SMC3 cause Cornelia de Lange syndrome, a developmental disorder characterized by intellectual and growth retardation, though SMC3 mutations typically produce less severe phenotypes than NIPBL mutations 4. SMC3 dysfunction also associates with holoprosencephaly and altered gene expression of developmental regulators 5, while elevated SMC3 expression in hepatocellular carcinoma correlates with poor prognosis and enhanced cell proliferation 6. Loss of cohesin components increases micronucleus formation, a hallmark of genomic instability 7.

Sources cited
1
SMC3 is a cohesin subunit; cohesin complex functions in sister chromatid segregation, non-cohesion-related roles in development and gene regulation
PMID: 31516082
2
ATM phosphorylates ESCO2, which acetylates SMC3 to stabilize cohesin and promote 53BP1 recruitment in DNA damage response
PMID: 37377435
3
GSK3 kinases regulate ESCO2-mediated SMC3 acetylation through MMS22L phosphorylation to control symmetric cohesion establishment
PMID: 36912084
4
SMC3 mutations cause Cornelia de Lange syndrome with variable severity; SMC3 variants produce less severe phenotypes than NIPBL mutations
PMID: 37377026
5
SMC3 variants associate with holoprosencephaly and aberrant expression of developmental genes (ZIC2, GLI2, SMAD3, FGFR1)
PMID: 31334757
6
SMC3 is upregulated in hepatocellular carcinoma; high SMC3 correlates with poor prognosis and RIT1-mediated proliferation via SMC3 acetylation
PMID: 38017479
7
Loss of cohesin components (DSCC1) increases micronucleus formation; SMC3 acetylation can be restored to rescue cohesinopathy phenotypes
PMID: 38355793
Disease Associationsβ“˜21
Cornelia de Lange syndromeOpen Targets
0.79Strong
genetic disorderOpen Targets
0.51Moderate
Wiedemann-Steiner syndromeOpen Targets
0.33Weak
cardiac arrestOpen Targets
0.32Weak
Intellectual disabilityOpen Targets
0.31Weak
neurodegenerative diseaseOpen Targets
0.30Weak
congenital heart diseaseOpen Targets
0.28Weak
autism spectrum disorderOpen Targets
0.26Weak
Neurodevelopmental disorderOpen Targets
0.12Weak
multiple congenital anomalies/dysmorphic syndromeOpen Targets
0.12Weak
neuromuscular diseaseOpen Targets
0.12Weak
hepatocellular carcinomaOpen Targets
0.09Suggestive
lymphomaOpen Targets
0.07Suggestive
neoplasmOpen Targets
0.07Suggestive
cystOpen Targets
0.06Suggestive
AnxietyOpen Targets
0.05Suggestive
Crohn's diseaseOpen Targets
0.04Suggestive
cerebral amyloid angiopathyOpen Targets
0.04Suggestive
acute myeloid leukemiaOpen Targets
0.04Suggestive
uncombable hair syndromeOpen Targets
0.03Suggestive
Cornelia de Lange syndrome 3 with or without midline brain defectsUniProt
Pathogenic Variants79
NM_005445.4(SMC3):c.3439C>G (p.Gln1147Glu)Pathogenic
Inborn genetic diseases|Cornelia de Lange syndrome 3
β˜…β˜…β˜†β˜†2025β†’ Residue 1147
NM_005445.4(SMC3):c.1417T>G (p.Trp473Gly)Likely pathogenic
not provided|Cornelia de Lange syndrome 3
β˜…β˜…β˜†β˜†2025β†’ Residue 473
NM_005445.4(SMC3):c.1942A>G (p.Met648Val)Pathogenic
not provided|Intellectual disability|Cornelia de Lange syndrome 3
β˜…β˜…β˜†β˜†2025β†’ Residue 648
NM_005445.4(SMC3):c.1450GCT[1] (p.Ala485del)Pathogenic
Cornelia de Lange syndrome 3|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 485
NM_005445.4(SMC3):c.587T>C (p.Ile196Thr)Pathogenic
Cornelia de Lange syndrome 3|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 196
NM_005445.4(SMC3):c.381C>G (p.Ser127Arg)Likely pathogenic
De Lange syndrome|Inborn genetic diseases
β˜…β˜…β˜†β˜†2023β†’ Residue 127
NM_005445.4(SMC3):c.283G>A (p.Glu95Lys)Likely pathogenic
Cornelia de Lange syndrome 3|De Lange syndrome
β˜…β˜…β˜†β˜†2015β†’ Residue 95
NM_005445.4(SMC3):c.717TGA[1] (p.Asp240del)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 240
NC_000010.11:g.110601022delLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_005445.4(SMC3):c.385G>C (p.Gly129Arg)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 129
NM_005445.4(SMC3):c.1943T>C (p.Met648Thr)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 648
NM_005445.4(SMC3):c.3454C>T (p.Gln1152Ter)Pathogenic
Cornelia de Lange syndrome 3
β˜…β˜†β˜†β˜†2025β†’ Residue 1152
NM_005445.4(SMC3):c.2242C>T (p.Gln748Ter)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 748
NM_005445.4(SMC3):c.2264C>G (p.Pro755Arg)Likely pathogenic
Cornelia de Lange syndrome 3
β˜…β˜†β˜†β˜†2025β†’ Residue 755
NM_005445.4(SMC3):c.2087T>C (p.Leu696Pro)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 696
NM_005445.4(SMC3):c.3104A>G (p.Gln1035Arg)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1035
NM_005445.4(SMC3):c.1078C>T (p.Arg360Ter)Likely pathogenic
Cornelia de Lange syndrome 3
β˜…β˜†β˜†β˜†2025β†’ Residue 360
NM_005445.4(SMC3):c.107C>A (p.Ser36Tyr)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 36
NM_005445.4(SMC3):c.1731T>G (p.Asn577Lys)Likely pathogenic
Cornelia de Lange syndrome 3
β˜…β˜†β˜†β˜†2024β†’ Residue 577
NM_005445.4(SMC3):c.2530G>T (p.Glu844Ter)Pathogenic
Cornelia de Lange syndrome 3
β˜…β˜†β˜†β˜†2024β†’ Residue 844
View on ClinVar β†—
Related Genes
MXI1Protein interaction100%ZNF143Protein interaction100%CHTF8Protein interaction100%RFC4Protein interaction100%DSCC1Protein interaction100%CHTF18Protein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
53%
Ovary
42%
Heart
40%
Lung
27%
Liver
19%
Gene Interaction Network
Click a node to explore
SMC3MXI1ZNF143CHTF8RFC4DSCC1CHTF18
PROTEIN STRUCTURE
Preparing viewer…
PDB8ROK Β· 2.25 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.13Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.08 [0.04–0.13]
RankingsWhere SMC3 stands among ~20K protein-coding genes
  • #1,180of 20,598
    Most Researched298 Β· top 10%
  • #935of 5,498
    Most Pathogenic Variants79 Β· top quartile
  • #143of 17,882
    Most Constrained (LOEUF)0.13 Β· top 1%
Genes detectedSMC3
Sources retrieved27 papers
Response timeβ€”
πŸ“„ Sources
27β–Ό
1
Genetic determinants of micronucleus formation in vivo.
PMID: 38355793
Nature Β· 2024
1.00
2
The expanding phenotypes of cohesinopathies: one ring to rule them all!
PMID: 31516082
Cell Cycle Β· 2019
0.90
3
Cornelia de Lange Spectrum.
PMID: 38735830
An Pediatr (Engl Ed) Β· 2024
0.84
4
Genomic analyses in Cornelia de Lange Syndrome and related diagnoses: Novel candidate genes, genotype-phenotype correlations and common mechanisms.
PMID: 37377026
Am J Med Genet A Β· 2023
0.80
5
ATM-ESCO2-SMC3 axis promotes 53BP1 recruitment in response to DNA damage and safeguards genome integrity by stabilizing cohesin complex.
PMID: 37377435
Nucleic Acids Res Β· 2023
0.70