X-linked intellectual disability - psychosis - macroorchidism: genes and variants
Explore variant evidence for X-linked intellectual disability - psychosis - macroorchidism across 1 analyzed protein (MECP2). Linked ClinVar records include 4 pathogenic or likely pathogenic variants, 8 variants of uncertain significance and 0 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. Source labels are pooled across this disease family.
Data updated 2026-10-10. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to X-linked intellectual disability - psychosis - macroorchidism
MECP2: Methyl-CpG-binding protein 2
It interprets DNA methylation and organizes transcriptional and chromatin states that are especially important in mature neurons. Loss-of-function variants cause Rett syndrome, whereas increased dosage causes MECP2 duplication syndrome.
4 ClinVar pathogenic / likely pathogenic and 8 uncertain variants in MECP2 have source records linked to X-linked intellectual disability - psychosis - macroorchidism. Association strength is not clinical gene validity.
ClinVar pathogenic and likely pathogenic variants linked to X-linked intellectual disability - psychosis - macroorchidism
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| MECP2 A140V | 140 | MBD | Pathogenic / likely pathogenic (★★★★) |
| MECP2 R106Q | 106 | MBD | Pathogenic / likely pathogenic (★★) |
| MECP2 P302A | 302 | Interaction with TBL1XR1 | Pathogenic / likely pathogenic (★★) |
| MECP2 L138F | 138 | MBD | Pathogenic / likely pathogenic (★) |
Same protein, different disease
- Rett syndrome also has ClinVar records linked to MECP2 variants; they fall mostly in different places as the X-linked intellectual disability - psychosis - macroorchidism variants (88 pathogenic / likely pathogenic).
- Severe neonatal-onset encephalopathy with microcephaly also has ClinVar records linked to MECP2 variants; they fall mostly in different places as the X-linked intellectual disability - psychosis - macroorchidism variants (29 pathogenic / likely pathogenic).
Diseases related to X-linked intellectual disability - psychosis - macroorchidism
- Rett syndrome, also linked to MECP2
- Severe neonatal-onset encephalopathy with microcephaly, also linked to MECP2
- Angelman syndrome, also linked to MECP2
- Autism, also linked to MECP2
- Focal epilepsy, also linked to MECP2
- Syndromic X-linked intellectual disability Lubs type, also linked to MECP2
Frequently asked questions
Which genes have records linked to X-linked intellectual disability - psychosis - macroorchidism?
This view contains 1 analyzed proteins: MECP2. 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 4 pathogenic or likely pathogenic variants, 8 variants of uncertain significance and 0 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 28 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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