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GeneE
6 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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SCRT2
scratch family transcriptional repressor 2
Chromosome 20 · 20p13
NCBI Gene: 85508Ensembl: ENSG00000215397.4HGNC: HGNC:15952UniProt: Q9NQ03
11PubMed Papers
16Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
sequence-specific double-stranded DNA bindingDNA-binding transcription factor activity, RNA polymerase II-specificDNA-binding transcription repressor activity, RNA polymerase II-specificE-box bindingAbruptio Placentaespondylolisthesisgastritishypertrophic cardiomyopathy
✦AI Summary

SCRT2 is a neural-specific zinc-finger transcription factor that functions as a transcriptional repressor of basic helix-loop-helix (bHLH) proteins during brain development 1. In the developing neocortex, SCRT2 is expressed in both mitotic progenitors and postmitotic neurons, where it negatively regulates bHLH transcription factors Ngn2/NeuroD1 on E-box-containing target genes 1. Mechanistically, SCRT2 promotes neuronal differentiation by favoring direct neurogenesis of radial glial progenitors while suppressing intermediate progenitor generation and delaying radial migration of upper layer neurons through repression of Rnd2, a key effector of neuronal migration 1. SCRT2 also mediates neuronal delamination from the apical neuroepithelium through transcriptional repression of E-cadherin, functioning as a molecular link between neuronal fate commitment and migration onset via an epithelial-mesenchymal transition-like mechanism 2. Clinically, SCRT2 has emerged as a biomarker for predicting recurrence risk in IDH-mutant gliomas; elevated SCRT2 expression is associated with increased risk of early recurrence in these lethal brain tumors and improves patient stratification when integrated with imaging and proteomic signatures 3. SCRT2 also exhibits epigenetic sensitivity, with DNA methylation near SCRT2 associated with high prenatal perfluorooctanoic acid exposure 4.

Sources cited
1
SCRT2 is a neural-specific zinc-finger transcription factor that modulates neurogenesis and cell migration by antagonizing bHLH proteins (Ngn2/NeuroD1) and regulating Rnd2 expression in the developing neocortex
PMID: 23180754
2
SCRT2 regulates neuronal migration onset through transcriptional repression of E-cadherin via an epithelial-mesenchymal transition-like mechanism
PMID: 23434913
3
SCRT2 is part of a gene signature associated with increased risk of early recurrence in IDH-mutant gliomas and improves patient stratification
PMID: 40214613
4
DNA methylation near SCRT2 is associated with high prenatal PFOA exposure in newborns
PMID: 33387539
⚠Limited data available — This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsⓘ16
Abruptio PlacentaeOpen Targets
0.31Weak
spondylolisthesisOpen Targets
0.23Weak
gastritisOpen Targets
0.22Weak
hypertrophic cardiomyopathyOpen Targets
0.05Suggestive
autismOpen Targets
0.02Suggestive
breast carcinomaOpen Targets
0.01Suggestive
ataxia telangiectasiaOpen Targets
0.01Suggestive
asthmaOpen Targets
0.01Suggestive
cardiovascular diseaseOpen Targets
0.00Suggestive
gliomaOpen Targets
0.00Suggestive
nonpapillary renal cell carcinomaOpen Targets
0.00Suggestive
renal cell carcinomaOpen Targets
0.00Suggestive
chronic kidney diseaseOpen Targets
0.00Suggestive
myelodysplastic syndromeOpen Targets
0.00Suggestive
atrial fibrillationOpen Targets
0.00Suggestive
cancerOpen Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
FAIMShared pathway33%GRINAShared pathway33%PEA15Shared pathway25%TMBIM1Shared pathway20%FAIM2Shared pathway13%RNF34Shared pathway13%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
1%
Heart
0%
Lung
0%
Ovary
0%
Liver
0%
Gene Interaction Network
Click a node to explore
SCRT2FAIMGRINAPEA15TMBIM1FAIM2RNF34
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q9NQ03
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.95LoF Tolerant
pLIⓘ
0.04Tolerant
Observed/Expected LoF2.34 [0.55–1.95]
RankingsWhere SCRT2 stands among ~20K protein-coding genes
  • #16,890of 20,598
    Most Researched11
  • #17,639of 17,882
    Most Constrained (LOEUF)1.95
Genes detectedSCRT2
Sources retrieved6 papers
Response time—
📄 Sources
6▼
1
Scratch2 modulates neurogenesis and cell migration through antagonism of bHLH proteins in the developing neocortex.
PMID: 23180754
Cereb Cortex · 2014
1.00
2
A strategy for multimodal integration of transcriptomics, proteomics, and radiomics data for the prediction of recurrence in patients with IDH-mutant gliomas.
PMID: 40214613
Int J Cancer · 2025
0.83
3
Perfluorooctanoic acid (PFOA) or perfluorooctane sulfonate (PFOS) and DNA methylation in newborn dried blood spots in the Upstate KIDS cohort.
PMID: 33387539
Environ Res · 2021
0.67
4
Abnormalities in endothelial form of nitric oxide synthase is pathogenic in limited cutaneous systemic sclerosis.
PMID: 30980594
J Cosmet Dermatol · 2019
0.50
5
Scratch regulates neuronal migration onset via an epithelial-mesenchymal transition-like mechanism.
PMID: 23434913
Nat Neurosci · 2013
0.33