Intellectual developmental disorder with seizures and language delay: genes and variants
Explore variant evidence for Intellectual developmental disorder with seizures and language delay across 1 analyzed protein (SETD1B). Linked ClinVar records include 13 pathogenic or likely pathogenic variants, 65 variants of uncertain significance and 7 with conflicting classifications.
Coverage includes proteins already analyzed in CATVariant, not every gene involved in this condition. Database links are associations, not an assessment of clinical gene–disease validity. Computable evidence prioritizes variants for expert review and does not reclassify them. Counts refer to the selected disease label.
Data updated 2026-10-11. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to Intellectual developmental disorder with seizures and language delay
SETD1B: Histone-lysine N-methyltransferase SETD1B
A histone methyltransferase that places H3K4 methyl marks and helps regulate gene expression. Pathogenic variants can cause a neurodevelopmental disorder with intellectual disability and seizures.
13 ClinVar pathogenic / likely pathogenic and 72 uncertain variants in SETD1B have source records linked to Intellectual developmental disorder with seizures and language delay. Association strength is not clinical gene validity.
Where Intellectual developmental disorder with seizures and language delay variants cluster
- SETD1B SET (positions 1827–1944): 3 of 13 ClinVar pathogenic / likely pathogenic variants, 3.8× more than its size predicts.
ClinVar pathogenic and likely pathogenic variants linked to Intellectual developmental disorder with seizures and language delay
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| SETD1B R1748C | 1748 | WDR5 interaction motif (WIN) | Pathogenic / likely pathogenic (★★) |
| SETD1B R1792Q | 1792 | Pathogenic / likely pathogenic (★★) | |
| SETD1B R1825W | 1825 | Pathogenic / likely pathogenic (★★) | |
| SETD1B R1902C | 1902 | SET | Pathogenic / likely pathogenic (★★) |
| SETD1B E1948K | 1948 | Pathogenic / likely pathogenic (★★) | |
| SETD1B R1748S | 1748 | WDR5 interaction motif (WIN) | Pathogenic / likely pathogenic (★) |
| SETD1B K1896E | 1896 | SET | Pathogenic / likely pathogenic (★) |
| SETD1B V129G | 129 | RRM | Pathogenic / likely pathogenic (★) |
| SETD1B S1795L | 1795 | Pathogenic / likely pathogenic (★) | |
| SETD1B R1885W | 1885 | SET | Pathogenic / likely pathogenic (★) |
| SETD1B C1954R | 1954 | Post-SET | Pathogenic / likely pathogenic (★) |
| SETD1B S1414Y | 1414 | Pathogenic / likely pathogenic (★) | |
| SETD1B A1129V | 1129 | Pathogenic / likely pathogenic |
Which prediction tools work for Intellectual developmental disorder with seizures and language delay
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- ESM1b (LLR): 96 out of 100
- CATVariant: 94 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- AlphaMissense: 94 out of 100
- SIFT: 77 out of 100
Diseases related to Intellectual developmental disorder with seizures and language delay
- Paediatric disorders, also linked to SETD1B
Frequently asked questions
Which genes have records linked to Intellectual developmental disorder with seizures and language delay?
This view contains 1 analyzed proteins: SETD1B. Links come from clinical records and association databases. They do not imply that every listed gene is a validated cause, and missing genes may not yet be analyzed.
What do the clinical classifications mean?
Linked records include 13 pathogenic or likely pathogenic variants, 65 variants of uncertain significance and 7 with conflicting classifications. Labels summarize source records; multi-condition records may not make a separate assertion for this disease. Check the original record and review status.
Does the evidence score change a VUS classification?
No. 0 VUS or conflicting variants reach the likely-pathogenic points range on the computable criteria available here. This is a research prioritization signal, not a clinical classification. Patient, family and other required evidence may be missing.
Can I download the variant evidence?
Download the CSV for all 94 variants in the selected disease scope, including clinical labels, review status, evidence criteria, predictor scores, functional measurements and population frequency where available.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from eligible public CATVariant analyses of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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