A465T

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

Alanine → Threonine at position 465 · Transmembrane helix 6 · WFS1 (Wolframin)

Interactive 3D Structure

Wild-type reference

Wild-type A465 — hydrogen bond to T461

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DynaMut2 mutant · A465T

Mutant T465 — hydrogen bond to L468 lost (3 contacts lost)

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Bond changes · DynaMut2 interaction analysis

3 lost2 gained8 preserved

Interaction type	Wild-type partner	Mutant partner	Status
Hydrogen bond	T461	T461	Preserved
Hydrogen bond	E462	E462	Preserved
Hydrogen bond	L468	—	Lost
Hydrogen bond	S469	S469	Preserved
Hydrogen bond	—	P504	Gained
Polar contact	T461	T461	Preserved
Polar contact	E462	E462	Preserved
Polar contact	L468	L468	Preserved
Polar contact	S469	S469	Preserved
Polar contact	—	P504	Gained
Van der Waals	T461	—	Lost
Van der Waals	E462	E462	Preserved
Hydrophobic	L507	—	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

-1.04kcal/mol

Destabilising — moderate

AlphaMissense

0.351

ambiguous

AlphaFold pLDDT

model confidence

Schema

Cat 4

Category 4 — Stable Fold, Function Disrupted

Clinical Evidence

ClinVar classificationUncertain significance

Review statuscriteria provided, multiple submitters, no conflicts

Associated conditionsWolfram syndrome 1; Inborn genetic diseases; Autosomal dominant nonsyndromic hearing loss 6; Type 2 diabetes mellitus; Wolfram-like syndrome; Cataract 41

Population frequency (gnomAD v4)Ultra-rare · AF 0.0036%

cDNA changec.1393G>A

ClinVar accessionVCV001003765

Last evaluated2025/07/27 00:00

Observed at very low frequency in gnomAD.

Full Variant Card

WFS1 Wolframin — A465T Variant Card

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

Alanine → Threonine at position 465. Transmembrane helix 6. ClinVar Uncertain significance, AlphaMissense 0.351, DynaMut2 ΔΔG -1.04 kcal/mol (destabilising).

Identity

Field	Value
Variant	A465T (p.Alanine465Threonine)
DNA change	c.1393G>A
Gene · Protein	WFS1 · Wolframin (890 aa)
UniProt	O76024 · WFS1_HUMAN
ClinVar accession	VCV001003765
Amino acid change	Alanine (A) → Threonine (T)

Structural Context

Field	Value
AlphaFold model	AF-O76024-F1, v6
pLDDT at residue 465	81.38 — well-folded
Domain	Transmembrane helix 6
Position context	Inside Transmembrane helix 6 · position 465 is bilayer-embedded
IDR flag	No — pLDDT above 50 threshold

UniProt features at this position:

(none catalogued)

Position 465 sits in a transmembrane helix (Transmembrane helix 6). Wolframin has eleven such helices anchoring it in the ER membrane; substitutions inside the bilayer-embedded segments can disrupt helix packing, lipid contacts, and the overall ER topology of the protein. The wild-type residue is small/hydrophobic (alanine — methyl sidechain); the mutant is small polar (threonine — hydroxyl). The chemistry shift implies altered local packing, hydrogen-bonding, and/or electrostatics at this site.

Computational Predictions

AlphaMissense

Field	Value
am_pathogenicity	0.3513
am_class	ambiguous
Interpretation	Likely benign (threshold 0.564)

DynaMut2

Field	Value
ΔΔG (kcal/mol)	-1.04 (Destabilising)
Job ID	178094704852
Result URL	https://biosig.lab.uq.edu.au/dynamut2/results_prediction/178094704852

Clinical Evidence

Field	Value
Classification	Uncertain significance
Review status	criteria provided, multiple submitters, no conflicts
Last evaluated	2025/07/27 00:00
Inheritance	Autosomal dominant pattern indicated by associated DFNA6/14/38 (WFS1 hearing loss 6).
WFS1 variant landscape	A465T is 1 of ~326 pathogenic-spectrum variants in WFS1 (out of 2,243 catalogued in ClinVar)

Wolfram syndrome 1
Inborn genetic diseases
Autosomal dominant nonsyndromic hearing loss 6
Type 2 diabetes mellitus
Wolfram-like syndrome
Cataract 41

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|=1.04 negligible. Likely site-specific functional disruption — docking strategy.

Why this card matters. Wolframin's fold survives this substitution (|ΔΔG|=1.04 kcal/mol). The pathogenic signal is real — AlphaMissense places it at 0.351. 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
A465T_molstar_viewer.html — interactive 3D viewer (auto-highlights position 465 with ball-and-stick + neighbors within 5Å)
A465T_variant_card.md — this card (source of truth)
A465T_variant_card.html — styled printable card
A465T_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)
A465T_wildtype_interactions.pse / A465T_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 A465T 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 A465T PDF card ↓Strategies are AI-generated predictions, not validated therapeutics.