Alpha thalassemia-X-linked intellectual disability syndrome: genes and variants
Explore variant evidence for Alpha thalassemia-X-linked intellectual disability syndrome across 1 analyzed protein (ATRX). Linked ClinVar records include 28 pathogenic or likely pathogenic variants, 451 variants of uncertain significance and 140 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 Alpha thalassemia-X-linked intellectual disability syndrome
ATRX: Chromatin remodeler ATRX
A chromatin-remodeling protein involved in transcriptional regulation and DNA replication, including at repetitive regions. Variants can cause ATR-X syndrome.
28 ClinVar pathogenic / likely pathogenic and 590 uncertain variants in ATRX have source records linked to Alpha thalassemia-X-linked intellectual disability syndrome. Association strength is not clinical gene validity.
Weakly linked (only a few uncertain records): GBA1.
Where Alpha thalassemia-X-linked intellectual disability syndrome variants cluster
- ATRX PHD-type (positions 217–272): 6 of 28 ClinVar pathogenic / likely pathogenic variants, 9.5× more than its size predicts.
- ATRX Interaction with MECP2 (positions 2010–2280): 10 of 28 ClinVar pathogenic / likely pathogenic variants, 3.3× more than its size predicts.
- ATRX Helicase ATP-binding (positions 1581–1768): 7 of 28 ClinVar pathogenic / likely pathogenic variants, 3.3× more than its size predicts.
ClinVar pathogenic and likely pathogenic variants linked to Alpha thalassemia-X-linked intellectual disability syndrome
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| ATRX C243W | 243 | ADD | Pathogenic / likely pathogenic (★★) |
| ATRX R2085H | 2085 | Helicase C-terminal | Pathogenic / likely pathogenic (★★) |
| ATRX R2131Q | 2131 | Helicase C-terminal | Pathogenic / likely pathogenic (★★) |
| ATRX R1661C | 1661 | Helicase ATP-binding | Pathogenic / likely pathogenic (★★) |
| ATRX Y1683C | 1683 | Helicase ATP-binding | Pathogenic / likely pathogenic (★★) |
| ATRX M1761V | 1761 | Helicase ATP-binding | Pathogenic / likely pathogenic (★★) |
| ATRX Y1847C | 1847 | Pathogenic / likely pathogenic (★★) | |
| ATRX R2178W | 2178 | Helicase C-terminal | Pathogenic / likely pathogenic (★★) |
| ATRX C243R | 243 | ADD | Pathogenic / likely pathogenic (★) |
| ATRX C243Y | 243 | ADD | Pathogenic / likely pathogenic (★) |
| ATRX H189Y | 189 | ADD | Pathogenic / likely pathogenic (★) |
| ATRX H1609Y | 1609 | Helicase ATP-binding | Pathogenic / likely pathogenic (★) |
| ATRX D2035G | 2035 | Helicase C-terminal | Pathogenic / likely pathogenic (★) |
| ATRX W222C | 222 | ADD | Pathogenic / likely pathogenic (★) |
| ATRX L253S | 253 | ADD | Pathogenic / likely pathogenic (★) |
| ATRX I1680T | 1680 | Helicase ATP-binding | Pathogenic / likely pathogenic (★) |
| ATRX A1790T | 1790 | Pathogenic / likely pathogenic (★) | |
| ATRX K1802T | 1802 | Pathogenic / likely pathogenic (★) | |
| ATRX T1884I | 1884 | Pathogenic / likely pathogenic (★) | |
| ATRX S2041N | 2041 | Helicase C-terminal | Pathogenic / likely pathogenic (★) |
| ATRX I2248T | 2248 | Interaction with MECP2 | Pathogenic / likely pathogenic (★) |
| ATRX E2265K | 2265 | Interaction with MECP2 | Pathogenic / likely pathogenic (★) |
| ATRX D2035V | 2035 | Helicase C-terminal | Pathogenic / likely pathogenic |
| ATRX K251E | 251 | ADD | Pathogenic / likely pathogenic |
| ATRX Y2084H | 2084 | Helicase C-terminal | Pathogenic / likely pathogenic |
| ATRX Y2163C | 2163 | Helicase C-terminal | Pathogenic / likely pathogenic |
| ATRX C1614R | 1614 | Helicase ATP-binding | Pathogenic / likely pathogenic |
| ATRX K1650N | 1650 | Helicase ATP-binding | Pathogenic / likely pathogenic |
Which prediction tools work for Alpha thalassemia-X-linked intellectual disability syndrome
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- MutPred2: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- CATVariant: 99 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- AlphaMissense: 98 out of 100
- ESM1b (LLR): 96 out of 100
- SIFT: 81 out of 100
- MetaLR: 77 out of 100 (learned from overlapping clinical labels, so this is optimistic)
Same protein, different disease
- Intellectual disability-hypotonic facies syndrome, X-linked, 1 also has ClinVar records linked to ATRX variants; they fall partly in the same places as the Alpha thalassemia-X-linked intellectual disability syndrome variants (16 pathogenic / likely pathogenic).
Diseases related to Alpha thalassemia-X-linked intellectual disability syndrome
- Intellectual disability-hypotonic facies syndrome, X-linked, 1, also linked to ATRX
- Male infertility with azoospermia or oligozoospermia due to single gene mutation, also linked to ATRX
- Microcephaly, also linked to ATRX
Frequently asked questions
Which genes have records linked to Alpha thalassemia-X-linked intellectual disability syndrome?
This view contains 1 analyzed proteins: ATRX. 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 28 pathogenic or likely pathogenic variants, 451 variants of uncertain significance and 140 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 941 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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