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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.
SETD5
SET domain containing 5
Chromosome 3 Β· 3p25.3
NCBI Gene: 55209Ensembl: ENSG00000168137.20HGNC: HGNC:25566UniProt: A0A804HKJ9
53PubMed Papers
21Diseases
0Drugs
268Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
nucleoplasmnucleushistone H3K9 methyltransferase activitySet3 complexintellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiencygenetic disorderIntellectual disabilityneurodegenerative disease
✦AI Summary

SETD5 is a chr3 regulator essential for normal brain development and cognitive function. As a lysine methyltransferase, SETD5 primarily facilitates H3K36 trimethylation (H3K36me3), which regulates RNA polymerase II elongation dynamics and transcriptional regulation 1. SETD5 interacts with the Hdac3 and Paf1 complexes to modulate gene expression patterns critical for neural development 2. Functionally, SETD5 controls neural stem cell proliferation and synaptic transmission through RNA elongation rate regulation 1. Pathogenic variants in SETD5 cause autosomal dominant intellectual developmental disorder-23 (IDEV23), representing one of the most common genetic causes of intellectual disability 3. The resulting SETD5-related neurodevelopmental disorder presents with intellectual disability or developmental delay (75% of cases), autism spectrum features (23.8% of individuals), hypotonia (39.2%), motor abnormalities including chorea and gait disturbances (35.7%), and seizures (14%) 4. Additional clinical features include dysmorphic facial features, brain abnormalities, and musculoskeletal defects, with variable penetrance particularly in females 5, 6. Setd5-haploinsufficient animal models demonstrate impaired cognition, abnormal brain-to-body ratios, and behavioral inflexibility, confirming the critical role of SETD5 in neural function 2.

Sources cited
1
SETD5 methylates histone H3 on lysine 36 and regulates transcription, euchromatin formation, RNA elongation and splicing
PMID: 36875494
2
Setd5-haploinsufficient mice show cognitive impairments, developmental defects, and altered expression of postsynaptic density proteins; SETD5 regulates RNA polymerase II dynamics via Hdac3 and Paf1 complexes
PMID: 30455454
3
SETD5 variants are among the most common causes of intellectual disability, found in ~3% of individuals with moderate to severe ID
PMID: 26350204
4
SETD5-related disorder presents with intellectual disability (75%), autism (23.8%), hypotonia (39.2%), motor abnormalities (35.7%), and seizures (14%)
PMID: 39603091
5
SETD5 mutations are associated with autism spectrum disorder, intellectual disability, and facial dysmorphism with variable penetrance in females
PMID: 29484850
6
SETD5 disorder features include intellectual disability, brain abnormalities, and musculoskeletal abnormalities; haploinsufficiency causes the phenotype
PMID: 40265665
Disease Associationsβ“˜21
intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiencyOpen Targets
0.82Strong
genetic disorderOpen Targets
0.55Moderate
Intellectual disabilityOpen Targets
0.51Moderate
neurodegenerative diseaseOpen Targets
0.45Moderate
Neurodevelopmental disorderOpen Targets
0.44Moderate
developmental disorder of mental healthOpen Targets
0.44Moderate
Neurodevelopmental abnormalityOpen Targets
0.42Moderate
KBG syndromeOpen Targets
0.42Moderate
type 2 diabetes mellitusOpen Targets
0.37Weak
Abnormal facial shapeOpen Targets
0.37Weak
complex neurodevelopmental disorderOpen Targets
0.37Weak
skeletal dysplasiaOpen Targets
0.37Weak
syndromic complex neurodevelopmental disorderOpen Targets
0.37Weak
cleft lipOpen Targets
0.34Weak
cleft palateOpen Targets
0.34Weak
3q26 microduplication syndromeOpen Targets
0.33Weak
Rare genetic intellectual disabilityOpen Targets
0.32Weak
autism spectrum disorderOpen Targets
0.30Weak
Neurodevelopmental delayOpen Targets
0.27Weak
tooth diseaseOpen Targets
0.27Weak
Intellectual developmental disorder, autosomal dominant 23UniProt
Pathogenic Variants268
NM_001080517.3(SETD5):c.2347-7A>GPathogenic
not provided|Inborn genetic diseases|See cases|Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency|Intellectual disability
β˜…β˜…β˜†β˜†2026
NM_001080517.3(SETD5):c.1709_1710del (p.Ser570fs)Pathogenic
Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency
β˜…β˜…β˜†β˜†2026β†’ Residue 570
NM_001080517.3(SETD5):c.2644C>T (p.Arg882Ter)Pathogenic
not provided|Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency|SETD5-related disorder|Inborn genetic diseases
β˜…β˜…β˜†β˜†2026β†’ Residue 882
NM_001080517.3(SETD5):c.1081C>T (p.Arg361Ter)Pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 361
NM_001080517.3(SETD5):c.1918C>T (p.Gln640Ter)Pathogenic
not provided|Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency
β˜…β˜…β˜†β˜†2025β†’ Residue 640
NM_001080517.3(SETD5):c.2003C>G (p.Ser668Ter)Pathogenic
Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency|not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 668
NM_001080517.3(SETD5):c.922C>T (p.Arg308Ter)Pathogenic
not provided|Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency|SETD5-related disorder|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 308
NM_001080517.3(SETD5):c.3001C>T (p.Arg1001Ter)Pathogenic
Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency|Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1001
NM_001080517.3(SETD5):c.3856del (p.Ser1286fs)Pathogenic
Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency|Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1286
NM_001080517.3(SETD5):c.1459G>T (p.Glu487Ter)Pathogenic
Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency
β˜…β˜…β˜†β˜†2025β†’ Residue 487
NM_001080517.3(SETD5):c.2302C>T (p.Arg768Ter)Pathogenic
Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency|Neurodevelopmental disorder|not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 768
NM_001080517.3(SETD5):c.1390C>T (p.Gln464Ter)Pathogenic
Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency|not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 464
NM_001080517.3(SETD5):c.2347-1G>APathogenic
not provided|Intellectual disability
β˜…β˜…β˜†β˜†2025
NM_001080517.3(SETD5):c.2734C>T (p.Arg912Ter)Pathogenic
Cornelia de Lange-like syndrome|not provided|Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency|Developmental disorder
β˜…β˜…β˜†β˜†2024β†’ Residue 912
NM_001080517.3(SETD5):c.972T>G (p.Phe324Leu)Likely pathogenic
Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency
β˜…β˜…β˜†β˜†2024β†’ Residue 324
NM_001080517.3(SETD5):c.3361C>T (p.Arg1121Ter)Pathogenic
not provided|Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency
β˜…β˜…β˜†β˜†2024β†’ Residue 1121
NM_001080517.3(SETD5):c.1333C>T (p.Arg445Ter)Pathogenic
not provided|Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency
β˜…β˜…β˜†β˜†2024β†’ Residue 445
NM_001080517.3(SETD5):c.2102del (p.Lys701fs)Pathogenic
not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 701
NM_001080517.3(SETD5):c.3301C>T (p.Gln1101Ter)Pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2024β†’ Residue 1101
NM_001080517.3(SETD5):c.3855dup (p.Ser1286fs)Pathogenic
not provided|Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency|Inborn genetic diseases
β˜…β˜…β˜†β˜†2024β†’ Residue 1286
View on ClinVar β†—
Related Genes
THUMPD3Protein interaction73%KMT2EProtein interaction70%SETD1AShared pathway29%CHD4Shared pathway22%MSL1Shared pathway20%HDGFL1Shared pathway20%
Tissue Expression6 tissues
Ovary
100%
Lung
91%
Liver
81%
Bone Marrow
67%
Heart
59%
Brain
51%
Gene Interaction Network
Click a node to explore
SETD5THUMPD3KMT2ESETD1ACHD4MSL1HDGFL1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9C0A6
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.38Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.29 [0.23–0.38]
RankingsWhere SETD5 stands among ~20K protein-coding genes
  • #8,489of 20,598
    Most Researched53
  • #235of 5,498
    Most Pathogenic Variants268 Β· top 5%
  • #1,788of 17,882
    Most Constrained (LOEUF)0.38 Β· top 10%
Genes detectedSETD5
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Targeted Next-Generation Sequencing Analysis of 1,000 Individuals with Intellectual Disability.
PMID: 26350204
Hum Mutat Β· 2015
1.00
2
Neurological and psychiatric phenotype of a multicenter cohort of patients with SETD5-related neurodevelopmental disorder.
PMID: 39603091
Eur J Paediatr Neurol Β· 2025
0.90
3
Structure, activity and function of the lysine methyltransferase SETD5.
PMID: 36875494
Front Endocrinol (Lausanne) Β· 2023
0.80
4
Expansion of the Genotypic and Phenotypic Spectrum of SETD5 Disorder Using Data From the National Brain Gene Registry.
PMID: 40265665
Clin Genet Β· 2025
0.70
5
De novo variants underlying monogenic syndromes with intellectual disability in a neurodevelopmental cohort from India.
PMID: 38114583
Eur J Hum Genet Β· 2024
0.60