Intellectual disability-hypotonic facies syndrome, X-linked, 1: genes and variants
Explore variant evidence for Intellectual disability-hypotonic facies syndrome, X-linked, 1 across 1 analyzed protein (ATRX). Linked ClinVar records include 16 pathogenic or likely pathogenic variants, 46 variants of uncertain significance and 22 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 2026-10-11. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to Intellectual disability-hypotonic facies syndrome, X-linked, 1
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.
16 ClinVar pathogenic / likely pathogenic and 68 uncertain variants in ATRX have source records linked to Intellectual disability-hypotonic facies syndrome, X-linked, 1. Association strength is not clinical gene validity.
Where Intellectual disability-hypotonic facies syndrome, X-linked, 1 variants cluster
- ATRX ADD (positions 159–296): 6 of 16 ClinVar pathogenic / likely pathogenic variants, 6.8× more than its size predicts.
- ATRX Helicase C-terminal (positions 2025–2205): 4 of 16 ClinVar pathogenic / likely pathogenic variants, 3.4× more than its size predicts.
- ATRX Helicase ATP-binding (positions 1581–1768): 4 of 16 ClinVar pathogenic / likely pathogenic variants, 3.3× more than its size predicts.
ClinVar pathogenic and likely pathogenic variants linked to Intellectual disability-hypotonic facies syndrome, X-linked, 1
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| ATRX R2131Q | 2131 | Helicase C-terminal | 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 P270L | 270 | ADD | Pathogenic / likely pathogenic (★) |
| ATRX P270R | 270 | ADD | Pathogenic / likely pathogenic (★) |
| ATRX S2043P | 2043 | Helicase C-terminal | Pathogenic / likely pathogenic (★) |
| ATRX R2085L | 2085 | Helicase C-terminal | Pathogenic / likely pathogenic (★) |
| ATRX H189Q | 189 | ADD | Pathogenic / likely pathogenic (★) |
| ATRX L253S | 253 | ADD | Pathogenic / likely pathogenic (★) |
| ATRX C280Y | 280 | ADD | Pathogenic / likely pathogenic (★) |
| ATRX L1656S | 1656 | Helicase ATP-binding | Pathogenic / likely pathogenic (★) |
| ATRX T1884I | 1884 | Pathogenic / likely pathogenic (★) | |
| ATRX C223R | 223 | ADD | Pathogenic / likely pathogenic |
| ATRX N1694D | 1694 | Helicase ATP-binding | Pathogenic / likely pathogenic |
| ATRX P1711S | 1711 | Helicase ATP-binding | Pathogenic / likely pathogenic |
Which prediction tools work for Intellectual disability-hypotonic facies syndrome, X-linked, 1
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- CATVariant: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- MutPred2: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- ESM1b (LLR): 100 out of 100
- AlphaMissense: 99 out of 100
- SIFT: 83 out of 100
- MetaLR: 78 out of 100 (learned from overlapping clinical labels, so this is optimistic)
Same protein, different disease
- Alpha thalassemia-X-linked intellectual disability syndrome also has ClinVar records linked to ATRX variants; they fall mostly in different places as the Intellectual disability-hypotonic facies syndrome, X-linked, 1 variants (28 pathogenic / likely pathogenic).
Diseases related to Intellectual disability-hypotonic facies syndrome, X-linked, 1
- Alpha thalassemia-X-linked intellectual disability syndrome, 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 Intellectual disability-hypotonic facies syndrome, X-linked, 1?
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 16 pathogenic or likely pathogenic variants, 46 variants of uncertain significance and 22 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 96 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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