Intellectual disability - sparse hair - brachydactyly: genes and variants
Explore variant evidence for Intellectual disability - sparse hair - brachydactyly across 1 analyzed protein (SMARCA2). Linked ClinVar records include 53 pathogenic or likely pathogenic variants, 43 variants of uncertain significance and 14 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 2026-10-21. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to Intellectual disability - sparse hair - brachydactyly
SMARCA2: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2
It provides ATP-dependent nucleosome remodeling activity to selected SWI/SNF complexes and helps control transcriptional access to chromatin. Heterozygous pathogenic variants cause Nicolaides-Baraitser syndrome or, through distinct mechanisms, blepharophimosis-intellectual-disability syndrome.
53 ClinVar pathogenic / likely pathogenic and 57 uncertain variants in SMARCA2 have source records linked to Intellectual disability - sparse hair - brachydactyly. Association strength is not clinical gene validity.
Where Intellectual disability - sparse hair - brachydactyly variants cluster
- SMARCA2 Helicase C-terminal (positions 1054–1216): 24 of 53 ClinVar pathogenic / likely pathogenic variants, 4.4× more than its size predicts.
- SMARCA2 DEGH box (positions 851–854): 4 of 53 ClinVar pathogenic / likely pathogenic variants, 30.0× more than its size predicts.
ClinVar pathogenic and likely pathogenic variants linked to Intellectual disability - sparse hair - brachydactyly
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| SMARCA2 S783L | 783 | Helicase ATP-binding | Pathogenic / likely pathogenic (★★) |
| SMARCA2 R855Q | 855 | Helicase ATP-binding | Pathogenic / likely pathogenic (★★) |
| SMARCA2 P883L | 883 | Helicase ATP-binding | Pathogenic / likely pathogenic (★★) |
| SMARCA2 R1162H | 1162 | Helicase C-terminal | Pathogenic / likely pathogenic (★★) |
| SMARCA2 S783W | 783 | Helicase ATP-binding | Pathogenic / likely pathogenic (★★) |
| SMARCA2 E852K | 852 | Helicase ATP-binding | Pathogenic / likely pathogenic (★★) |
| SMARCA2 P883Q | 883 | Helicase ATP-binding | Pathogenic / likely pathogenic (★★) |
| SMARCA2 R1105H | 1105 | Helicase C-terminal | Pathogenic / likely pathogenic (★★) |
| SMARCA2 R1105P | 1105 | Helicase C-terminal | Pathogenic / likely pathogenic (★★) |
| SMARCA2 R1105C | 1105 | Helicase C-terminal | Pathogenic / likely pathogenic (★★) |
| SMARCA2 R1159G | 1159 | Helicase C-terminal | Pathogenic / likely pathogenic (★★) |
| SMARCA2 R1159Q | 1159 | Helicase C-terminal | Pathogenic / likely pathogenic (★★) |
| SMARCA2 R1162C | 1162 | Helicase C-terminal | Pathogenic / likely pathogenic (★★) |
| SMARCA2 A1201V | 1201 | Helicase C-terminal | Pathogenic / likely pathogenic (★★) |
| SMARCA2 A1160G | 1160 | Helicase C-terminal | Pathogenic / likely pathogenic (★★) |
| SMARCA2 R937H | 937 | Pathogenic / likely pathogenic (★★) | |
| SMARCA2 T1321M | 1321 | Pathogenic / likely pathogenic (★★) | |
| SMARCA2 D534Y | 534 | Pathogenic / likely pathogenic (★★) | |
| SMARCA2 G1129D | 1129 | Helicase C-terminal | Pathogenic / likely pathogenic (★★) |
| SMARCA2 E852Q | 852 | Helicase ATP-binding | Pathogenic / likely pathogenic (★) |
| SMARCA2 Q1165K | 1165 | Helicase C-terminal | Pathogenic / likely pathogenic (★) |
| SMARCA2 G1164R | 1164 | Helicase C-terminal | Pathogenic / likely pathogenic (★) |
| SMARCA2 L946F | 946 | Pathogenic / likely pathogenic (★) | |
| SMARCA2 H1161R | 1161 | Helicase C-terminal | Pathogenic / likely pathogenic (★) |
| SMARCA2 Q1200P | 1200 | Helicase C-terminal | Pathogenic / likely pathogenic (★) |
| SMARCA2 L529V | 529 | Pathogenic / likely pathogenic (★) | |
| SMARCA2 G752R | 752 | Helicase ATP-binding | Pathogenic / likely pathogenic (★) |
| SMARCA2 L753H | 753 | Helicase ATP-binding | Pathogenic / likely pathogenic (★) |
| SMARCA2 T829I | 829 | Helicase ATP-binding | Pathogenic / likely pathogenic (★) |
| SMARCA2 R844Q | 844 | Helicase ATP-binding | Pathogenic / likely pathogenic (★) |
| SMARCA2 W912C | 912 | Pathogenic / likely pathogenic (★) | |
| SMARCA2 P944Q | 944 | Pathogenic / likely pathogenic (★) | |
| SMARCA2 K951N | 951 | Pathogenic / likely pathogenic (★) | |
| SMARCA2 T989R | 989 | Pathogenic / likely pathogenic (★) | |
| SMARCA2 Q1074E | 1074 | Helicase C-terminal | Pathogenic / likely pathogenic (★) |
| SMARCA2 G1098S | 1098 | Helicase C-terminal | Pathogenic / likely pathogenic (★) |
| SMARCA2 H1151Y | 1151 | Helicase C-terminal | Pathogenic / likely pathogenic (★) |
| SMARCA2 Q1196P | 1196 | Helicase C-terminal | Pathogenic / likely pathogenic (★) |
| SMARCA2 A1219P | 1219 | Pathogenic / likely pathogenic (★) | |
| SMARCA2 R420C | 420 | Pathogenic / likely pathogenic (★) | |
| SMARCA2 R855G | 855 | Helicase ATP-binding | Pathogenic / likely pathogenic |
| SMARCA2 R1159L | 1159 | Helicase C-terminal | Pathogenic / likely pathogenic |
| SMARCA2 Q1165H | 1165 | Helicase C-terminal | Pathogenic / likely pathogenic |
| SMARCA2 W795R | 795 | Helicase ATP-binding | Pathogenic / likely pathogenic |
| SMARCA2 D851G | 851 | Helicase ATP-binding | Pathogenic / likely pathogenic |
| SMARCA2 H854L | 854 | Helicase ATP-binding | Pathogenic / likely pathogenic |
| SMARCA2 G881V | 881 | Helicase ATP-binding | Pathogenic / likely pathogenic |
| SMARCA2 D1158V | 1158 | Helicase C-terminal | Pathogenic / likely pathogenic |
| SMARCA2 G1202C | 1202 | Helicase C-terminal | Pathogenic / likely pathogenic |
| SMARCA2 H939Y | 939 | Pathogenic / likely pathogenic | |
| SMARCA2 G1132D | 1132 | Helicase C-terminal | Pathogenic / likely pathogenic |
| SMARCA2 D1147E | 1147 | Helicase C-terminal | Pathogenic / likely pathogenic |
| SMARCA2 R1306K | 1306 | Pathogenic / likely pathogenic |
Uncertain variants prioritized for review in Intellectual disability - sparse hair - brachydactyly
| Variant | Position | Protein part | Clinical label | Evidence |
|---|---|---|---|---|
| SMARCA2 P944L | 944 | Uncertain (★) | +6: 2 other pathogenic changes within 3 positions; P944Q at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 1.00 |
Which prediction tools work for Intellectual disability - sparse hair - brachydactyly
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- REVEL: 99 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- AlphaMissense: 99 out of 100
- EVE: 98 out of 100
- CATVariant: 96 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- MetaSVM: 96 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- SIFT: 95 out of 100
- MutPred2: 95 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- CADD: 95 out of 100
- MetaLR: 95 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- ESM1b (LLR): 95 out of 100
- PolyPhen-2: 85 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- phyloP: 77 out of 100
- SpliceAI: 58 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- Pangolin: 53 out of 100 (learned from overlapping clinical labels, so this is optimistic)
Same protein, different disease
- Blepharophimosis-impaired intellectual development syndrome also has ClinVar records linked to SMARCA2 variants; they fall partly in the same places as the Intellectual disability - sparse hair - brachydactyly variants (8 pathogenic / likely pathogenic).
Diseases related to Intellectual disability - sparse hair - brachydactyly
- Blepharophimosis-impaired intellectual development syndrome, also linked to SMARCA2
- Pituitary stalk interruption syndrome, also linked to SMARCA2
Frequently asked questions
Which genes have records linked to Intellectual disability - sparse hair - brachydactyly?
This view contains 1 analyzed proteins: SMARCA2. 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 53 pathogenic or likely pathogenic variants, 43 variants of uncertain significance and 14 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. 1 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 146 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.
Download every variant as CSV · Browse all diseases · Methods · About the Center