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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
DEAF1
DEAF1 transcription factor
Chromosome 11 Β· 11p15.5
NCBI Gene: 10522Ensembl: ENSG00000177030.19HGNC: HGNC:14677UniProt: A0A804HIS1
61PubMed Papers
22Diseases
0Drugs
103Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
positive regulation of DNA-templated transcriptionnegative regulation of transcription by RNA polymerase IIfibrillar centerDNA-binding transcription repressor activity, RNA polymerase II-specificintellectual disability, autosomal dominant 24intellectual disability-epilepsy-extrapyramidal syndromeintellectual developmental disorder with paroxysmal dyskinesia or seizuresgenetic disorder
✦AI Summary

DEAF1 is a multifunctional transcription factor that regulates gene expression through binding to unmethylated CpG-containing DNA sequences 1. Primary functions include transcriptional repression of specific genes via sequence-specific binding to motifs like 5'-TTC[CG]G-3' 1, and activation of genes including EIF4G3 and the 5-HT1A receptor through both direct and indirect mechanisms 2. Mechanistically, DEAF1 acts downstream of FOXO signaling to regulate muscle regeneration and aging by suppressing autophagy genes PIK3C3 and ATG16L1 34. Exercise-induced FOXO activation suppresses DEAF1 expression, normalizing mTORC1 activity and reversing muscle aging 4. DEAF1 phosphorylation by GSK3Ξ² regulates 5-HT1A repression, with lithium inhibiting this pathway 2. Disease relevance spans neurodevelopmental and muscular domains. De novo variants cause DEAF1-associated neurodevelopmental disorder (DAND) with intellectual disability, speech delay, autism, and sleep disturbances through dominant-negative mechanisms, while biallelic variants additionally cause microcephaly with partial loss of function 56. DEAF1 promotes hepatocellular carcinoma progression by enhancing glutamine transporter expression and reducing oxidative stress 7. Clinically, detailed phenotypic analysis and functional studies are essential for variant pathogenicity determination in DAND patients 5, while FOXO-DEAF1-mTORC1 axis modulation offers therapeutic potential for sarcopenia and age-related muscle loss 4.

Sources cited
1
De novo DEAF1 variants cause neurodevelopmental disorder with intellectual disability, speech delay, motor delay, autism, and sleep disturbances; microcephaly is exclusive to recessive variants
PMID: 30923367
2
DEAF1 is transcriptionally repressed by FOXO and suppresses autophagy genes PIK3C3 and ATG16L1; DEAF1 depletion increases autophagy and impairs muscle regeneration
PMID: 38963021
3
De novo DEAF1 variants in DNA binding domain display dominant negative activity affecting genes involved in neuronal function and dendritic spine maintenance
PMID: 35981081
4
DEAF1 acts as presynaptic repressor of 5-HT1A transcription; GSK3Ξ² phosphorylates and regulates DEAF1 activity; lithium inhibits this pathway
PMID: 37958600
5
Exercise suppresses DEAF1 via FOXO activation, restoring mTORC1 balance and alleviating muscle aging; DEAF1 elevation increases mTOR transcription
PMID: 41284871
6
DEAF1 binds unmethylated, variably spaced CpG dinucleotides within consensus sequence; CpG methylation abolishes binding
PMID: 25531106
7
DEAF1 rs11246280 SNP is associated with hepatocellular carcinoma susceptibility; DEAF1 enhances glutamine transporter expression and reduces oxidative stress
PMID: 40554679
Disease Associationsβ“˜22
intellectual disability, autosomal dominant 24Open Targets
0.79Strong
intellectual disability-epilepsy-extrapyramidal syndromeOpen Targets
0.70Strong
intellectual developmental disorder with paroxysmal dyskinesia or seizuresOpen Targets
0.55Moderate
genetic disorderOpen Targets
0.51Moderate
Neurodevelopmental delayOpen Targets
0.41Moderate
autism spectrum disorderOpen Targets
0.36Weak
autismOpen Targets
0.34Weak
autosomal dominant non-syndromic intellectual disabilityOpen Targets
0.27Weak
developmental disorder of mental healthOpen Targets
0.27Weak
Intellectual disabilityOpen Targets
0.15Weak
Familial prostate cancerOpen Targets
0.11Weak
prostate cancerOpen Targets
0.11Weak
skull disorderOpen Targets
0.07Suggestive
response to statinOpen Targets
0.07Suggestive
HyperglycemiaOpen Targets
0.06Suggestive
AnxietyOpen Targets
0.06Suggestive
interstitial lung diseaseOpen Targets
0.06Suggestive
diaphanospondylodysostosisOpen Targets
0.06Suggestive
cancerOpen Targets
0.05Suggestive
neural tube defects, folate-sensitiveOpen Targets
0.05Suggestive
Neurodevelopmental disorder with hypotonia, impaired expressive language, and with or without seizuresUniProt
Vulto-van Silfout-de Vries syndromeUniProt
Pathogenic Variants103
NM_021008.4(DEAF1):c.1450C>T (p.Arg484Ter)Pathogenic
not provided|DEAF1-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 484
NM_021008.4(DEAF1):c.926del (p.Leu309fs)Pathogenic
Intellectual disability, autosomal dominant 24|not provided|DEAF1-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 309
NM_021008.4(DEAF1):c.706A>G (p.Ser236Gly)Likely pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 236
NM_021008.4(DEAF1):c.634G>A (p.Gly212Ser)Pathogenic
Intellectual disability, autosomal dominant 24|not provided|Intellectual disability, autosomal dominant 24;Intellectual disability-epilepsy-extrapyramidal syndrome|Neurodevelopmental delay
β˜…β˜…β˜†β˜†2025β†’ Residue 212
NM_021008.4(DEAF1):c.837C>G (p.Cys279Trp)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 279
NM_021008.4(DEAF1):c.553C>T (p.Gln185Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 185
NM_021008.4(DEAF1):c.34_35dup (p.Leu13fs)Pathogenic
Intellectual disability, autosomal dominant 24|not provided|Intellectual disability-epilepsy-extrapyramidal syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 13
NM_021008.4(DEAF1):c.701G>A (p.Trp234Ter)Pathogenic
not provided|Intellectual disability-epilepsy-extrapyramidal syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 234
NM_021008.4(DEAF1):c.676C>T (p.Arg226Trp)Pathogenic
Intellectual disability-epilepsy-extrapyramidal syndrome|Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 226
NM_021008.4(DEAF1):c.1104_1105dup (p.Asp369fs)Pathogenic
Intellectual disability-epilepsy-extrapyramidal syndrome|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 369
NM_021008.4(DEAF1):c.781C>T (p.Arg261Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 261
NM_021008.4(DEAF1):c.671G>C (p.Arg224Pro)Pathogenic
not provided|Intellectual disability, autosomal dominant 24
β˜…β˜…β˜†β˜†2024β†’ Residue 224
NM_021008.4(DEAF1):c.748A>G (p.Lys250Glu)Pathogenic
Intellectual disability, autosomal dominant 24|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 250
NM_021008.4(DEAF1):c.670C>T (p.Arg224Trp)Pathogenic
Intellectual disability, autosomal dominant 24|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 224
NM_021008.4(DEAF1):c.998-2A>GLikely pathogenic
not provided
β˜…β˜…β˜†β˜†2022
NM_021008.4(DEAF1):c.737G>C (p.Arg246Thr)Pathogenic
Intellectual disability, autosomal dominant 24
β˜…β˜…β˜†β˜†2021β†’ Residue 246
NM_021008.4(DEAF1):c.700T>G (p.Trp234Gly)Pathogenic
not provided
β˜…β˜…β˜†β˜†2019β†’ Residue 234
NM_021008.4(DEAF1):c.842G>C (p.Cys281Ser)Likely pathogenic
Intellectual disability, autosomal dominant 24
β˜…β˜…β˜†β˜†2018β†’ Residue 281
NM_021008.4(DEAF1):c.1011dup (p.Ser338fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2026β†’ Residue 338
NM_021008.4(DEAF1):c.907C>T (p.Arg303Cys)Pathogenic
not provided
β˜…β˜†β˜†β˜†2026β†’ Residue 303
View on ClinVar β†—
Related Genes
ZMYND11Protein interaction89%ZMYND19Protein interaction81%GCM1Shared pathway25%ZNF141Shared pathway25%GLIS3Shared pathway14%CCDC124Shared pathway14%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
74%
Ovary
51%
Heart
42%
Liver
39%
Lung
34%
Gene Interaction Network
Click a node to explore
DEAF1ZMYND11ZMYND19GCM1ZNF141GLIS3CCDC124
PROTEIN STRUCTURE
Preparing viewer…
PDB5UWW Β· 2.15 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.18LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.94 [0.76–1.18]
RankingsWhere DEAF1 stands among ~20K protein-coding genes
  • #7,547of 20,598
    Most Researched61
  • #752of 5,498
    Most Pathogenic Variants103 Β· top quartile
  • #12,373of 17,882
    Most Constrained (LOEUF)1.18
Genes detectedDEAF1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
De novo and biallelic DEAF1 variants cause a phenotypic spectrum.
PMID: 30923367
Genet Med Β· 2019
1.00
2
FOXO-regulated DEAF1 controls muscle regeneration through autophagy.
PMID: 38963021
Autophagy Β· 2024
0.90
3
SMYD2-Methylated PPARΞ³ Facilitates Hypoxia-Induced Pulmonary Hypertension by Activating Mitophagy.
PMID: 38770649
Circ Res Β· 2024
0.80
4
Expansion and mechanistic insights into de novo DEAF1 variants in DEAF1-associated neurodevelopmental disorders.
PMID: 35981081
Hum Mol Genet Β· 2023
0.70
5
Transcriptional Regulation of the Human 5-HT1A Receptor Gene by Lithium: Role of Deaf1 and GSK3Ξ².
PMID: 37958600
Int J Mol Sci Β· 2023
0.60