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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.
SETBP1
SET binding protein 1
Chromosome 18 Β· 18q12.3
NCBI Gene: 26040Ensembl: ENSG00000152217.20HGNC: HGNC:15573UniProt: A0A7I2V4X1
86PubMed Papers
26Diseases
0Drugs
126Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
nucleoplasmnucleusprotein bindingnuclear membraneSchinzel-Giedion syndromeintellectual disability, autosomal dominant 29chronic myelogenous leukemiamyelodysplastic syndrome
✦AI Summary

SETBP1 encodes a transcription factor with broad tissue expression involved in transcriptional regulation and DNA binding 1. The gene functions in both germline and somatic disease contexts through distinct molecular mechanisms. Germline loss-of-function variants cause haploinsufficiency-associated neurodevelopmental disorders, including SETBP1-haploinsufficiency disorder characterized by intellectual disability with loss of expressive language 2, and the severe pediatric condition Schinzel-Giedion syndrome 1. Somatic SETBP1 mutations drive myeloid malignancies, particularly enriched in atypical chr18 myeloid leukemia (aCML) and chr18 neutrophilic leukemia (CNL) 3. In aCML, SETBP1 mutations frequently co-occur with ASXL1 and other myeloid driver mutations, forming disease-specific mutational signatures 4. SETBP1 mutations also accumulate during disease progression from myelodysplastic syndrome to secondary CNL 5. Tissue-specific analysis reveals SETBP1 and its targets show coordinated expression patterns across 31 human tissues with distinct functional enrichment in transcriptional regulation and mitochondrial function 1. Germline variants additionally predispose to clonal hematopoiesis 6. SETBP1 mutations correlate with adverse prognosis in myeloid neoplasms, supporting its role as a clinically relevant molecular marker in diagnosis and risk stratification 3.

Sources cited
1
SETBP1 is a transcription factor with tissue-specific expression patterns and target gene activity across 31 human tissues; germline variants cause SGS and SETBP1-HD
PMID: 37873221
2
SETBP1 haploinsufficiency is associated with intellectual disability and loss of expressive language in developmental delay
PMID: 25217958
3
SETBP1 mutations are enriched in aCML and support diagnosis; SETBP1 mutations are associated with adverse prognosis in myeloid neoplasms
PMID: 38644693
4
ASXL1-SETBP1 co-mutations are specific to aCML; SETBP1 mutations impact outcome in MDS/MPN subtypes
PMID: 32573691
5
SETBP1 mutations accumulate during progression from MDS to CNL and can be tracked during disease development
PMID: 37439996
6
Germline variants at SETBP1 locus predispose to clonal hematopoiesis and increase risk of myeloproliferative neoplasia
PMID: 35835912
Disease Associationsβ“˜26
Schinzel-Giedion syndromeOpen Targets
0.81Strong
intellectual disability, autosomal dominant 29Open Targets
0.73Strong
chronic myelogenous leukemiaOpen Targets
0.66Moderate
myelodysplastic syndromeOpen Targets
0.66Moderate
acute myeloid leukemiaOpen Targets
0.66Moderate
genetic disorderOpen Targets
0.52Moderate
Intellectual disabilityOpen Targets
0.50Moderate
Juvenile Myelomonocytic LeukemiaOpen Targets
0.49Moderate
hearing lossOpen Targets
0.49Moderate
hypertensionOpen Targets
0.48Moderate
Sensorineural hearing impairmentOpen Targets
0.48Moderate
breast carcinomaOpen Targets
0.48Moderate
KeloidOpen Targets
0.41Moderate
Crohn's diseaseOpen Targets
0.39Weak
bundle branch blockOpen Targets
0.39Weak
sleep apneaOpen Targets
0.39Weak
Complete right bundle branch blockOpen Targets
0.39Weak
non-small cell lung carcinomaOpen Targets
0.39Weak
cardiovascular diseaseOpen Targets
0.39Weak
Chronic Neutrophilic LeukemiaOpen Targets
0.38Weak
Intellectual developmental disorder, autosomal dominant 29UniProt
Leukemia, acute myelogenousUniProt
Leukemia, chronic myeloid, atypicalUniProt
Leukemia, juvenile myelomonocyticUniProt
Myelodysplastic syndromeUniProt
Schinzel-Giedion midface retraction syndromeUniProt
Pathogenic Variants126
NM_015559.3(SETBP1):c.666G>A (p.Trp222Ter)Pathogenic
not provided|Intellectual disability, autosomal dominant 29
β˜…β˜…β˜†β˜†2025β†’ Residue 222
NM_015559.3(SETBP1):c.2608G>A (p.Gly870Ser)Pathogenic
Schinzel-Giedion syndrome|not provided|SETBP1-related disorder|Intellectual disability, autosomal dominant 29
β˜…β˜…β˜†β˜†2025β†’ Residue 870
NM_015559.3(SETBP1):c.2425C>T (p.Gln809Ter)Pathogenic
Intellectual disability, autosomal dominant 29|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 809
NM_015559.3(SETBP1):c.1765C>T (p.Arg589Ter)Pathogenic
not provided|Intellectual disability, autosomal dominant 29|Schinzel-Giedion syndrome;Intellectual disability, autosomal dominant 29|Inborn genetic diseases|Intellectual disability
β˜…β˜…β˜†β˜†2025β†’ Residue 589
NM_015559.3(SETBP1):c.3211del (p.Ala1071fs)Pathogenic
SETBP1-related disorder|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1071
NM_015559.3(SETBP1):c.1630C>T (p.Arg544Ter)Pathogenic
not provided|Intellectual disability, autosomal dominant 29
β˜…β˜…β˜†β˜†2025β†’ Residue 544
NM_015559.3(SETBP1):c.1876C>T (p.Arg626Ter)Pathogenic
Intellectual disability, autosomal dominant 29|not provided|Schinzel-Giedion syndrome;Intellectual disability, autosomal dominant 29|SETBP1-related disorder|Intellectual disability
β˜…β˜…β˜†β˜†2024β†’ Residue 626
NM_015559.3(SETBP1):c.2572G>A (p.Glu858Lys)Pathogenic
Inborn genetic diseases|Intellectual disability, autosomal dominant 29|not provided|Schinzel-Giedion syndrome|See cases
β˜…β˜…β˜†β˜†2024β†’ Residue 858
NM_015559.3(SETBP1):c.821G>A (p.Trp274Ter)Pathogenic
not provided|Intellectual disability, autosomal dominant 29
β˜…β˜…β˜†β˜†2024β†’ Residue 274
NM_015559.3(SETBP1):c.2607C>G (p.Ser869Arg)Pathogenic
Schinzel-Giedion syndrome|SETBP1-related disorder
β˜…β˜…β˜†β˜†2024β†’ Residue 869
NM_015559.3(SETBP1):c.1588C>T (p.Arg530Ter)Pathogenic
Developmental disorder|Intellectual disability, autosomal dominant 29|SETBP1-related disorder|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 530
NM_015559.3(SETBP1):c.2665C>T (p.Arg889Ter)Pathogenic
Abnormality of the nervous system|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 889
NM_015559.3(SETBP1):c.2602G>C (p.Asp868His)Pathogenic
Schinzel-Giedion syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 868
NM_015559.3(SETBP1):c.1873C>T (p.Arg625Ter)Pathogenic
Intellectual disability, autosomal dominant 29|not provided|Schinzel-Giedion syndrome;Intellectual disability, autosomal dominant 29
β˜…β˜…β˜†β˜†2023β†’ Residue 625
NM_015559.3(SETBP1):c.2601C>A (p.Ser867Arg)Pathogenic
Schinzel-Giedion syndrome|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 867
NM_015559.3(SETBP1):c.2602G>A (p.Asp868Asn)Pathogenic
Schinzel-Giedion syndrome|not provided|Intellectual disability, autosomal dominant 29;Schinzel-Giedion syndrome|Intellectual disability, autosomal dominant 29|SETBP1-related disorder
β˜…β˜…β˜†β˜†2023β†’ Residue 868
NM_015559.3(SETBP1):c.2612T>C (p.Ile871Thr)Pathogenic
Schinzel-Giedion syndrome|not provided|Intellectual disability, autosomal dominant 29|Fetal akinesia deformation sequence 1;Arthrogryposis multiplex congenita|SETBP1-related disorder
β˜…β˜…β˜†β˜†2023β†’ Residue 871
NM_015559.3(SETBP1):c.44dup (p.Glu16fs)Pathogenic
not provided|Intellectual disability, autosomal dominant 29
β˜…β˜…β˜†β˜†2022β†’ Residue 16
NM_015559.3(SETBP1):c.2017_2018del (p.Lys673fs)Pathogenic
not provided
β˜…β˜…β˜†β˜†2022β†’ Residue 673
NM_015559.3(SETBP1):c.1408del (p.Lys469_Met470insTer)Pathogenic
Inborn genetic diseases|Intellectual disability, autosomal dominant 29|not provided
β˜…β˜…β˜†β˜†2021β†’ Residue 469
View on ClinVar β†—
Related Genes
MSL1Shared pathway100%HDGFL1Shared pathway100%HIPK4Shared pathway100%HMGB4Shared pathway100%NAA40Shared pathway100%NSD1Shared pathway100%
Tissue Expression6 tissues
Brain
100%
Ovary
56%
Lung
47%
Heart
32%
Liver
31%
Bone Marrow
10%
Gene Interaction Network
Click a node to explore
SETBP1MSL1HDGFL1HIPK4HMGB4NAA40NSD1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9Y6X0
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.14Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.08 [0.05–0.14]
RankingsWhere SETBP1 stands among ~20K protein-coding genes
  • #5,572of 20,598
    Most Researched86
  • #622of 5,498
    Most Pathogenic Variants126 Β· top quartile
  • #178of 17,882
    Most Constrained (LOEUF)0.14 Β· top 1%
Genes detectedSETBP1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Chronic neutrophilic leukemia preceded by myelodysplastic syndromes.
PMID: 37439996
Int J Hematol Β· 2023
1.00
2
Refining analyses of copy number variation identifies specific genes associated with developmental delay.
PMID: 25217958
Nat Genet Β· 2014
0.90
3
Classification and mutation prediction from non-small cell lung cancer histopathology images using deep learning.
PMID: 30224757
Nat Med Β· 2018
0.80
4
Genomics of myelodysplastic syndrome/myeloproliferative neoplasm overlap syndromes.
PMID: 33275756
Hematology Am Soc Hematol Educ Program Β· 2020
0.70
5
Chronic neutrophilic leukemia and atypical chronic myeloid leukemia: 2024 update on diagnosis, genetics, risk stratification, and management.
PMID: 38644693
Am J Hematol Β· 2024
0.60