HomeAboutRankingsData Sources
Β© 2026 GeneE
🧬
GeneE
10 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.
SMARCAL1
SNF2 related chromatin remodeling annealing helicase 1
Chromosome 2 Β· 2q35
NCBI Gene: 50485Ensembl: ENSG00000138375.15HGNC: HGNC:11102UniProt: Q9NZC9
105PubMed Papers
21Diseases
0Drugs
165Pathogenic Variants
FUNCTIONAL ROLE
DNA Repair
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
DNA replication factor A complexprotein bindingdouble-strand break repair via nonhomologous end joiningregulation of transcription by RNA polymerase IISchimke immuno-osseous dysplasiafocal segmental glomerulosclerosissteroid-resistant nephrotic syndromemicrocephaly
✦AI Summary

SMARCAL1 is an ATP-dependent DNA translocase that plays a critical role in maintaining genome stability during DNA replication stress 1. The protein functions as an annealing helicase that catalyzes the rewinding of stably unwound DNA and binds selectively to fork DNA structures 1. SMARCAL1 participates in replication fork reversal, a mechanism that helps cells tolerate replication stress by reannealing parental template DNA strands 1. The protein exhibits profound synthetic lethality with FANCM, another DNA translocase, with their combined loss causing severe genome instability and chromosome 2 at loci enriched in simple repeats 2. SMARCAL1 also directly unwinds TA-rich DNA cruciforms, preventing catastrophic chromosome 2 3. Additionally, SMARCAL1 has specialized functions at telomeres, where it limits DNA damage during replication of difficult-to-replicate telomere sequences, with deficient cells displaying extrachromosomal telomere circles and DNA damage markers 4. Clinically, SMARCAL1 mutations cause Schimke immuno-osseous dysplasia and have been identified as causative mutations in steroid-resistant nephrotic syndrome 5. The protein's regulation is crucial, as RAD52 can restrict SMARCAL1-mediated fork reversal through competitive binding mechanisms 6.

Sources cited
1
SMARCAL1 is an ATP-dependent DNA translocase involved in replication fork reversal
PMID: 39089193
2
SMARCAL1 shows synthetic lethality with FANCM and prevents genome instability
PMID: 39510066
3
SMARCAL1 directly unwinds TA-rich DNA cruciforms preventing chromosome breakage
PMID: 40205037
4
SMARCAL1 mutations cause steroid-resistant nephrotic syndrome
PMID: 29127259
5
SMARCAL1 functions at telomeres to limit DNA damage during replication
PMID: 27355316
6
RAD52 restricts SMARCAL1-mediated fork reversal through competitive mechanisms
PMID: 40175552
Disease Associationsβ“˜21
Schimke immuno-osseous dysplasiaOpen Targets
0.84Strong
focal segmental glomerulosclerosisOpen Targets
0.47Moderate
steroid-resistant nephrotic syndromeOpen Targets
0.43Moderate
microcephalyOpen Targets
0.43Moderate
Decreased body weightOpen Targets
0.43Moderate
Disproportionate short-trunk short statureOpen Targets
0.43Moderate
familial atrioventricular septal defectOpen Targets
0.43Moderate
Primary microcephalyOpen Targets
0.43Moderate
Short statureOpen Targets
0.43Moderate
Small for gestational ageOpen Targets
0.43Moderate
osteoarthritis, hipOpen Targets
0.40Moderate
nephrotic syndromeOpen Targets
0.39Weak
immunodeficiency diseaseOpen Targets
0.36Weak
medical procedureOpen Targets
0.32Weak
atypical hemolytic-uremic syndromeOpen Targets
0.29Weak
type 1 diabetes mellitusOpen Targets
0.21Weak
genetic disorderOpen Targets
0.19Weak
kidney diseaseOpen Targets
0.17Weak
cancerOpen Targets
0.10Suggestive
Blackfan-Diamond anemiaOpen Targets
0.08Suggestive
Schimke immuno-osseous dysplasiaUniProt
Pathogenic Variants165
NM_014140.4(SMARCAL1):c.1682G>A (p.Arg561His)Pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2026β†’ Residue 561
NM_014140.4(SMARCAL1):c.2542G>T (p.Glu848Ter)Pathogenic
Schimke immuno-osseous dysplasia|9 conditions|Nephrotic syndrome|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 848
NM_014140.4(SMARCAL1):c.2459G>A (p.Arg820His)Pathogenic
Inherited Immunodeficiency Diseases|Schimke immuno-osseous dysplasia|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 820
NM_014140.4(SMARCAL1):c.1930C>T (p.Arg644Trp)Pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2026β†’ Residue 644
NM_014140.4(SMARCAL1):c.2070+2dupPathogenic
Schimke immuno-osseous dysplasia|not provided
β˜…β˜…β˜†β˜†2025
NM_014140.4(SMARCAL1):c.2321C>A (p.Ser774Ter)Pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 774
NM_014140.4(SMARCAL1):c.1933C>T (p.Arg645Cys)Pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 645
NM_014140.4(SMARCAL1):c.863-2A>GPathogenic
not provided|Schimke immuno-osseous dysplasia|SMARCAL1-related disorder|Familial cancer of breast
β˜…β˜…β˜†β˜†2025
NM_014140.4(SMARCAL1):c.1000C>T (p.Arg334Ter)Pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 334
NM_014140.4(SMARCAL1):c.2291G>A (p.Arg764Gln)Pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 764
NM_014140.4(SMARCAL1):c.415_416del (p.Leu139fs)Pathogenic
not provided|Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 139
NM_014140.4(SMARCAL1):c.1687C>T (p.Arg563Ter)Pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 563
NM_014140.4(SMARCAL1):c.1934_1935del (p.Arg645fs)Pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 645
NM_014140.4(SMARCAL1):c.622del (p.His208fs)Pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 208
NM_014140.4(SMARCAL1):c.1334+1G>APathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025
NM_014140.4(SMARCAL1):c.1736C>T (p.Ser579Leu)Pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 579
NM_014140.4(SMARCAL1):c.1485+1G>ALikely pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025
NM_014140.4(SMARCAL1):c.609del (p.Asn203fs)Pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 203
NM_014140.4(SMARCAL1):c.1934G>A (p.Arg645His)Pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 645
NM_014140.4(SMARCAL1):c.1190del (p.Leu397fs)Pathogenic
Schimke immuno-osseous dysplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 397
View on ClinVar β†—
Related Genes
STN1Protein interaction100%TIPINProtein interaction100%RPA1Protein interaction100%RPA2Protein interaction100%RPA3Protein interaction100%WRNProtein interaction100%
Tissue Expression6 tissues
Ovary
100%
Brain
72%
Heart
70%
Lung
67%
Bone Marrow
62%
Liver
50%
Gene Interaction Network
Click a node to explore
SMARCAL1STN1TIPINRPA1RPA2RPA3WRN
PROTEIN STRUCTURE
Preparing viewer…
PDB4MQV Β· 1.95 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.80LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.64 [0.51–0.80]
RankingsWhere SMARCAL1 stands among ~20K protein-coding genes
  • #4,563of 20,598
    Most Researched105 Β· top quartile
  • #453of 5,498
    Most Pathogenic Variants165 Β· top 10%
  • #6,580of 17,882
    Most Constrained (LOEUF)0.80
Genes detectedSMARCAL1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Mechanisms and regulation of replication fork reversal.
PMID: 39089193
DNA Repair (Amst) Β· 2024
1.00
2
Profound synthetic lethality between SMARCAL1 and FANCM.
PMID: 39510066
Mol Cell Β· 2024
0.90
3
Comprehensive interrogation of synthetic lethality in the DNA damage response.
PMID: 40205037
Nature Β· 2025
0.80
4
Whole Exome Sequencing of Patients with Steroid-Resistant Nephrotic Syndrome.
PMID: 29127259
Clin J Am Soc Nephrol Β· 2018
0.70
5
Temporally distinct post-replicative repair mechanisms fill PRIMPOL-dependent ssDNA gaps in human cells.
PMID: 34624216
Mol Cell Β· 2021
0.60