V258A

Category 4 — Stable Fold, Function DisruptedUncertain significanceCytoplasmic · predictedSource card

Valine → Alanine at position 258 · N-terminal cytoplasmic (intrinsically disordered) · WFS1 (Wolframin)

Interactive 3D Structure

Wild-type reference

Wild-type V258 — hydrogen bond to K253

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DynaMut2 mutant · V258A

Mutant A258 — hydrophobic contact to K256 lost

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Bond changes · DynaMut2 interaction analysis

1 lost2 gained4 preserved

Interaction type	Wild-type partner	Mutant partner	Status
Hydrogen bond	K253	K253	Preserved
Hydrogen bond	—	Y254	Gained
Hydrogen bond	P260	P260	Preserved
Polar contact	K253	K253	Preserved
Carbonyl	—	K253	Gained
Hydrophobic	K253	K253	Preserved
Hydrophobic	K256	—	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

DynaMut2 ΔΔG

-0.45kcal/mol

Destabilising — mild

AlphaMissense

0.379

ambiguous

AlphaFold pLDDT

model confidence

Schema

Cat 4

Category 4 — Stable Fold, Function Disrupted

Clinical Evidence

ClinVar classificationUncertain significance

Review statuscriteria provided, single submitter

Associated conditions—

Population frequency (gnomAD v4)Ultra-rare · AF 0.00037%

cDNA changec.773T>C

ClinVar accessionVCV001981666

Last evaluated2023/08/04 00:00

Observed at very low frequency in gnomAD.

Full Variant Card

WFS1 Wolframin — V258A Variant Card

Molecular Atlas Pilot · RareResearch.AI · Generated by wolfram-variant-card skill

Valine → Alanine at position 258. N-terminal cytoplasmic (intrinsically disordered). ClinVar Uncertain significance, AlphaMissense 0.379, DynaMut2 ΔΔG -0.45 kcal/mol (destabilising).

Identity

Field	Value
Variant	V258A (p.Valine258Alanine)
DNA change	c.773T>C
Gene · Protein	WFS1 · Wolframin (890 aa)
UniProt	O76024 · WFS1_HUMAN
ClinVar accession	VCV001981666
Amino acid change	Valine (V) → Alanine (A)

Structural Context

Field	Value
AlphaFold model	AF-O76024-F1, v6
pLDDT at residue 258	71.44 — well-folded
Domain	N-terminal cytoplasmic (intrinsically disordered)
Position context	N-terminal cytoplasmic (intrinsically disordered)
IDR flag	No — pLDDT above 50 threshold

UniProt features at this position:

(none catalogued)

Position 258 sits in N-terminal cytoplasmic (intrinsically disordered). The wild-type residue is small hydrophobic (valine — branched); the mutant is small/hydrophobic (alanine — methyl sidechain). The chemistry shift implies altered local packing, hydrogen-bonding, and/or electrostatics at this site.

Computational Predictions

AlphaMissense

Field	Value
am_pathogenicity	0.3791
am_class	ambiguous
Interpretation	Likely benign (threshold 0.564)

DynaMut2

Field	Value
ΔΔG (kcal/mol)	-0.45 (Destabilising)
Job ID	178094718214
Result URL	https://biosig.lab.uq.edu.au/dynamut2/results_prediction/178094718214

Clinical Evidence

Field	Value
Classification	Uncertain significance
Review status	criteria provided, single submitter
Last evaluated	2023/08/04 00:00
Inheritance	Inheritance pattern not specified in ClinVar entry; WFS1 has both AD and AR presentations.
WFS1 variant landscape	V258A 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 4 — Stable Fold, Function Disrupted

<strong>Category 4 — Stable Fold, Function Disrupted</strong><br/><br/>|ΔΔG|=0.45 negligible. Likely site-specific functional disruption — docking strategy.

Why this card matters. Wolframin's fold survives this substitution (|ΔΔG|=0.45 kcal/mol). The pathogenic signal is real — AlphaMissense places it at 0.379. Protein still folds, but a specific local site is broken. Pharmacological chaperones and small-molecule binders are the rational therapeutic vector.

Files in this folder

AF-O76024-F1-model_v6.pdb — AlphaFold structure
V258A_molstar_viewer.html — interactive 3D viewer (auto-highlights position 258 with ball-and-stick + neighbors within 5Å)
V258A_variant_card.md — this card (source of truth)
V258A_variant_card.html — styled printable card
V258A_dynamut2_summary.html — clean offline DynaMut2 result card
dynamut2_result.json — structured result data
dynamut2_result_page.html — local snapshot of the Biosig result page (asset URLs absolutized)
V258A_wildtype_interactions.pse / V258A_mutant_interactions.pse — PyMOL sessions

Generated by wolfram-variant-card skill · RareResearch.AI Molecular Atlas Every assumption documented. Every score sourced.

Therapeutic Strategy Handoff · prediction

Feed this card to Wolfram Intelligence

Download the V258A 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.

Download V258A PDF card ↓Strategies are AI-generated predictions, not validated therapeutics.