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GeneE
25 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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SMC1A
structural maintenance of chromosomes 1A
Chromosome X Β· Xp11.22
NCBI Gene: 8243Ensembl: ENSG00000072501.19HGNC: HGNC:11111UniProt: A0A384MR33
340PubMed Papers
22Diseases
0Drugs
217Pathogenic Variants
FUNCTIONAL ROLE
DNA RepairHighly ConstrainedHub Gene
RESEARCH IMPACT
Highly StudiedTrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
response to DNA damage checkpoint signalingmitotic spindle assemblyRNA bindingprotein bindingCornelia de Lange syndromegenetic developmental and epileptic encephalopathygenetic disorderEpileptic encephalopathy
✦AI Summary

SMC1A encodes a core structural subunit of the cohesin complex, a ring-shaped protein assembly essential for sister chrX cohesion during mitosis and meiosis 1. The cohesin complex physically tethers replicated DNA strands together until anaphase, when proteolytic cleavage allows chromosome X 1. Beyond its canonical cohesion function, SMC1A participates in gene transcription regulation, genome organization, and DNA damage repair through phosphorylation by ATM and ATR kinases 1. Additionally, SMC1A is involved in median forebrain development, with expression in prosencephalic neural folds during primary neurulation 2. Pathogenic SMC1A variants cause multiple developmental disorders. Heterozygous or hemizygous mutations are associated with Cornelia de Lange syndrome (CdLS), a multisystem developmental disorder characterized by intellectual disability, growth retardation, and distinctive facial features 3. More recently, SMC1A variants have been identified in developmental and epileptic encephalopathy 85 with or without midline brain defects 4, and loss-of-function variants in X-linked holoprosencephaly 2. SMC1A dysregulation also has cancer relevance; the gene is overexpressed in chrX unstable colorectal cancer, and SMC1A silencing combined with bevacizumab demonstrates therapeutic potential 5. Current evidence indicates SMC1A variants result in residual protein function rather than complete loss 6.

Sources cited
1
SMC1A encodes a cohesin subunit involved in sister chromatid cohesion, gene transcription, genome organization, and DNA damage repair through ATM/ATR phosphorylation
PMID: 32222533
2
SMC1A loss-of-function variants cause holoprosencephaly; SMC1A and STAG2 are expressed in prosencephalic neural folds during neurulation
PMID: 31334757
3
Heterozygous or hemizygous SMC1A variants contribute to Cornelia de Lange syndrome with variable severity
PMID: 37377026
4
SMC1A variants are associated with developmental and epileptic encephalopathy 85
PMID: 38612920
5
SMC1A is overexpressed in colorectal cancer; SMC1A knockdown reduces proliferation and enhances bevacizumab efficacy
PMID: 38365745
6
SMC1A mutations reported to date are missense or small in-frame deletions maintaining open reading frame, suggesting residual protein function
PMID: 19842212
Disease Associationsβ“˜22
Cornelia de Lange syndromeOpen Targets
0.79Strong
genetic developmental and epileptic encephalopathyOpen Targets
0.72Strong
genetic disorderOpen Targets
0.53Moderate
Epileptic encephalopathyOpen Targets
0.50Moderate
atypical Rett syndromeOpen Targets
0.45Moderate
Wiedemann-Steiner syndromeOpen Targets
0.42Moderate
microcephalyOpen Targets
0.41Moderate
X-linked complex neurodevelopmental disorderOpen Targets
0.40Weak
Global developmental delayOpen Targets
0.37Weak
semilobar holoprosencephalyOpen Targets
0.37Weak
SeizureOpen Targets
0.34Weak
Abnormal heart valve morphologyOpen Targets
0.34Weak
HirsutismOpen Targets
0.34Weak
HypertoniaOpen Targets
0.34Weak
Progressive sensorineural hearing impairmentOpen Targets
0.34Weak
Intellectual disabilityOpen Targets
0.30Weak
acute myeloid leukemiaOpen Targets
0.28Weak
Abnormality of the nervous systemOpen Targets
0.27Weak
hepatocellular carcinomaOpen Targets
0.21Weak
colon adenocarcinomaOpen Targets
0.19Weak
Cornelia de Lange syndrome 2UniProt
Developmental and epileptic encephalopathy 85 with or without midline brain defectsUniProt
Pathogenic Variants217
NM_006306.4(SMC1A):c.2853_2856del (p.Ser951fs)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|not provided|Developmental and epileptic encephalopathy, 85, with or without midline brain defects
β˜…β˜…β˜†β˜†2025β†’ Residue 951
NM_006306.4(SMC1A):c.1495C>T (p.Arg499Ter)Pathogenic
not provided|SMC1A-related cohesinopathy|Congenital muscular hypertrophy-cerebral syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 499
NM_006306.4(SMC1A):c.2351T>C (p.Ile784Thr)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 784
NM_006306.4(SMC1A):c.1193G>A (p.Arg398Gln)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 398
NM_006306.4(SMC1A):c.2948A>G (p.Tyr983Cys)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 983
NM_006306.4(SMC1A):c.2368C>T (p.Arg790Trp)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|Microcephaly|Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 790
NM_006306.4(SMC1A):c.2078G>A (p.Arg693Gln)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 693
NM_006306.4(SMC1A):c.1486C>T (p.Arg496Cys)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|not provided|Congenital muscular hypertrophy-cerebral syndrome;Developmental and epileptic encephalopathy, 85, with or without midline brain defects
β˜…β˜…β˜†β˜†2024β†’ Residue 496
NM_006306.4(SMC1A):c.547_548del (p.Gln183fs)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|SMC1A-related disorder
β˜…β˜…β˜†β˜†2024β†’ Residue 183
NM_006306.4(SMC1A):c.1877G>A (p.Arg626His)Likely pathogenic
Congenital muscular hypertrophy-cerebral syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 626
NM_006306.4(SMC1A):c.3103C>T (p.Arg1035Ter)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|Inborn genetic diseases
β˜…β˜…β˜†β˜†2024β†’ Residue 1035
NM_006306.4(SMC1A):c.2132G>A (p.Arg711Gln)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|not provided|Developmental and epileptic encephalopathy, 85, with or without midline brain defects;Congenital muscular hypertrophy-cerebral syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 711
NM_006306.4(SMC1A):c.157dup (p.Thr53fs)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 53
NM_006306.4(SMC1A):c.511C>T (p.Arg171Ter)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 171
NM_006306.4(SMC1A):c.2329T>C (p.Phe777Leu)Pathogenic
Inborn genetic diseases|Congenital muscular hypertrophy-cerebral syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 777
NM_006306.4(SMC1A):c.2173C>T (p.Arg725Ter)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|Epileptic encephalopathy
β˜…β˜…β˜†β˜†2024β†’ Residue 725
NM_006306.4(SMC1A):c.2161C>T (p.Gln721Ter)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|Developmental and epileptic encephalopathy, 85, with or without midline brain defects
β˜…β˜…β˜†β˜†2023β†’ Residue 721
NM_006306.4(SMC1A):c.1114-2A>GPathogenic
Congenital muscular hypertrophy-cerebral syndrome
β˜…β˜…β˜†β˜†2023
NM_006306.4(SMC1A):c.2890_2893del (p.Ser964fs)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|Developmental and epileptic encephalopathy, 85, with or without midline brain defects
β˜…β˜…β˜†β˜†2023β†’ Residue 964
NM_006306.4(SMC1A):c.3146G>A (p.Arg1049Gln)Pathogenic
Congenital muscular hypertrophy-cerebral syndrome|not provided|Congenital muscular hypertrophy-cerebral syndrome;Developmental and epileptic encephalopathy, 85, with or without midline brain defects
β˜…β˜…β˜†β˜†2023β†’ Residue 1049
View on ClinVar β†—
Related Genes
PDS5AProtein interaction100%ATMProtein interaction100%NCAPGProtein interaction100%SMC2Protein interaction100%NCAPD2Protein interaction100%MDC1Protein interaction100%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
57%
Heart
55%
Ovary
42%
Lung
39%
Liver
33%
Gene Interaction Network
Click a node to explore
SMC1APDS5AATMNCAPGSMC2NCAPD2MDC1
PROTEIN STRUCTURE
Preparing viewer…
PDB8ROE Β· 1.36 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.10Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.04 [0.02–0.10]
RankingsWhere SMC1A stands among ~20K protein-coding genes
  • #948of 20,598
    Most Researched340 Β· top 5%
  • #304of 5,498
    Most Pathogenic Variants217 Β· top 10%
  • #48of 17,882
    Most Constrained (LOEUF)0.10 Β· top 1%
Genes detectedSMC1A
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
X-Linked Epilepsies: A Narrative Review.
PMID: 38612920
Int J Mol Sci 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
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
4
Sulfotransferase SULT2B1 facilitates colon cancer metastasis by promoting SCD1-mediated lipid metabolism.
PMID: 38372484
Clin Transl Med Β· 2024
0.70
5
SMC1A epilepsy syndrome: clinical data from a large international cohort.
PMID: 38421079
Am J Med Genet A Β· 2024
0.68