G656S
Category 5 — IDR ExclusionUncertain significanceLumenal · predictedσ-1 candidateSource cardInteractive 3D Structure
Bond changes · DynaMut2 interaction analysis
| Interaction type | Wild-type partner | Mutant partner | Status |
|---|---|---|---|
| Hydrogen bond | R653 | R653 | Preserved |
| Hydrogen bond | K658 | K658 | Preserved |
| Polar contact | R653 | R653 | Preserved |
| Polar contact | S654 | S654 | Preserved |
| Polar contact | K658 | K658 | Preserved |
| Van der Waals | — | S654 | Gained |
| Van der Waals | K658 | — | Lost |
Lost / gained / preserved interatomic contacts at the variant residue, from the DynaMut2 (Arpeggio) interaction analysis of the wild-type and energy-minimized mutant structures.
Computational Predictions
Clinical Evidence
Observed at very low frequency in gnomAD.
Full Variant Card
WFS1 Wolframin — G656S Variant Card
Molecular Atlas Pilot · RareResearch.AI · Generated by wolfram-variant-card skill
Glycine → Serine at position 656. C-terminal ER-lumenal (calcium binding. ClinVar Uncertain significance, AlphaMissense 0.511, DynaMut2 ΔΔG -0.06 kcal/mol (destabilising).
Identity
| Field | Value |
|---|---|
| Variant | G656S (p.Glycine656Serine) |
| DNA change | c.1966G>A |
| Gene · Protein | WFS1 · Wolframin (890 aa) |
| UniProt | O76024 · WFS1_HUMAN |
| ClinVar accession | VCV001014101 |
| Amino acid change | Glycine (G) → Serine (S) |
Structural Context
| Field | Value |
|---|---|
| AlphaFold model | AF-O76024-F1, v6 |
| pLDDT at residue 656 | 48.88 — IDR (below 50 threshold) |
| Domain | C-terminal ER-lumenal (calcium binding, calmodulin, chaperone) |
| Position context | C-terminal lumenal domain · position 656 projects into the ER lumen |
| IDR flag | YES — pLDDT below 50 (Cat 5) |
UniProt features at this position:
(none catalogued)
Position 656 sits in the C-terminal lumenal domain (residues 653–869), wolframin's largest soluble region. This domain projects into the ER lumen and is implicated in calcium handling, ER stress sensing, and protein–protein interactions with ATF6 and Na+/K+ ATPase β1. The wild-type residue is small/flexible (glycine — backbone flexibility, no sidechain); the mutant is small polar (serine — hydroxyl). The chemistry shift implies altered local packing, hydrogen-bonding, and/or electrostatics at this site.
Computational Predictions
AlphaMissense
| Field | Value |
|---|---|
| am_pathogenicity | 0.5107 |
| am_class | ambiguous |
| Interpretation | Likely benign (threshold 0.564) |
DynaMut2
| Field | Value |
|---|---|
| ΔΔG (kcal/mol) | -0.06 (Destabilising) |
| Job ID | 178094713787 |
| Result URL | https://biosig.lab.uq.edu.au/dynamut2/results_prediction/178094713787 |
Clinical Evidence
| Field | Value |
|---|---|
| Classification | Uncertain significance |
| Review status | criteria provided, multiple submitters, no conflicts |
| Last evaluated | 2025/04/22 00:00 |
| Inheritance | Inheritance pattern not specified in ClinVar entry; WFS1 has both AD and AR presentations. |
| WFS1 variant landscape | G656S is 1 of ~326 pathogenic-spectrum variants in WFS1 (out of 2,243 catalogued in ClinVar) |
(no conditions catalogued)
Research Path Decision Tree
ΔΔG < 2 + binding site affected → CATEGORY 3 — docking experiments
ΔΔG 2–4 → CATEGORY 2 — pharmacological chaperones
ΔΔG > 4 → CATEGORY 1 — gene therapy
pLDDT < 50 → CATEGORY 5 — IDR, experimental only
Stable fold + functional site hit → CATEGORY 4 — site-specific docking
Final Schema Categorization
Category 5 — IDR Exclusion
<strong>Category 5 — IDR Exclusion</strong><br/><br/>pLDDT 48.88 is below 50; DynaMut2 result not trustworthy. Route to wet-lab.
Why this card matters. Position sits in a low-confidence region. Computational stability estimates here are unreliable; this variant needs experimental characterization before any therapeutic strategy is set.
Files in this folder
AF-O76024-F1-model_v6.pdb— AlphaFold structureG656S_molstar_viewer.html— interactive 3D viewer (auto-highlights position 656 with ball-and-stick + neighbors within 5Å)G656S_variant_card.md— this card (source of truth)G656S_variant_card.html— styled printable cardG656S_dynamut2_summary.html— clean offline DynaMut2 result carddynamut2_result.json— structured result datadynamut2_result_page.html— local snapshot of the Biosig result page (asset URLs absolutized)G656S_wildtype_interactions.pse/G656S_mutant_interactions.pse— PyMOL sessions
Generated by wolfram-variant-card skill · RareResearch.AI Molecular Atlas Every assumption documented. Every score sourced.
Feed this card to Wolfram Intelligence
Download the G656S PDF below and upload it to Wolfram Intelligence to generate therapeutic-strategy proposals — guanidinium mimetics, sigma-1 agonist docking, NAC thiol-capping. NAC is already on the bench-testing list.