S605N

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

Serine → Asparagine at position 605 · C-terminal ER-lumenal (calcium binding, calmodulin, chaperone) · WFS1 (Wolframin)

Interactive 3D Structure

Wild-type reference

Wild-type S605 — hydrogen bond to V601

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DynaMut2 mutant · S605N

Mutant N605 — hydrogen bond contact to A602 lost

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Bond changes · DynaMut2 interaction analysis

1 lost1 gained11 preserved

Interaction type	Wild-type partner	Mutant partner	Status
Hydrogen bond	V601	V601	Preserved
Hydrogen bond	A602	A602	Preserved
Hydrogen bond	L608	L608	Preserved
Hydrogen bond	L609	L609	Preserved
Polar contact	V601	V601	Preserved
Polar contact	A602	A602	Preserved
Polar contact	V603	V603	Preserved
Polar contact	L608	L608	Preserved
Polar contact	L609	L609	Preserved
Van der Waals	V601	V601	Preserved
Van der Waals	V603	—	Lost
Van der Waals	L609	L609	Preserved
Hydrophobic	—	L609	Gained

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

-0.07kcal/mol

Destabilising — mild

AlphaMissense

0.458

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 conditions—

Population frequency (gnomAD v4)Ultra-rare · AF 0.00055%

cDNA changec.1814G>A

ClinVar accessionVCV002415162

Last evaluated2024/06/07 00:00

Observed at very low frequency in gnomAD.

Full Variant Card

WFS1 Wolframin — S605N Variant Card

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

Serine → Asparagine at position 605. C-terminal ER-lumenal (calcium binding. ClinVar Uncertain significance, AlphaMissense 0.458, DynaMut2 ΔΔG -0.07 kcal/mol (destabilising).

Identity

Field	Value
Variant	S605N (p.Serine605Asparagine)
DNA change	c.1814G>A
Gene · Protein	WFS1 · Wolframin (890 aa)
UniProt	O76024 · WFS1_HUMAN
ClinVar accession	VCV002415162
Amino acid change	Serine (S) → Asparagine (N)

Structural Context

Field	Value
AlphaFold model	AF-O76024-F1, v6
pLDDT at residue 605	74.12 — well-folded
Domain	C-terminal ER-lumenal (calcium binding, calmodulin, chaperone)
Position context	C-terminal lumenal domain · position 605 projects into the ER lumen
IDR flag	No — pLDDT above 50 threshold

UniProt features at this position:

(none catalogued)

Position 605 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 polar (serine — hydroxyl); the mutant is polar amide (asparagine — H-bond donor/acceptor). The chemistry shift implies altered local packing, hydrogen-bonding, and/or electrostatics at this site.

Computational Predictions

AlphaMissense

Field	Value
am_pathogenicity	0.4575
am_class	ambiguous
Interpretation	Likely benign (threshold 0.564)

DynaMut2

Field	Value
ΔΔG (kcal/mol)	-0.07 (Destabilising)
Job ID	178094705896
Result URL	https://biosig.lab.uq.edu.au/dynamut2/results_prediction/178094705896

Clinical Evidence

Field	Value
Classification	Uncertain significance
Review status	criteria provided, multiple submitters, no conflicts
Last evaluated	2024/06/07 00:00
Inheritance	Inheritance pattern not specified in ClinVar entry; WFS1 has both AD and AR presentations.
WFS1 variant landscape	S605N 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|=0.07 negligible. Likely site-specific functional disruption — docking strategy.

Why this card matters. Wolframin's fold survives this substitution (|ΔΔG|=0.07 kcal/mol). The pathogenic signal is real — AlphaMissense places it at 0.458. 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
S605N_molstar_viewer.html — interactive 3D viewer (auto-highlights position 605 with ball-and-stick + neighbors within 5Å)
S605N_variant_card.md — this card (source of truth)
S605N_variant_card.html — styled printable card
S605N_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)
S605N_wildtype_interactions.pse / S605N_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 S605N 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 S605N PDF card ↓Strategies are AI-generated predictions, not validated therapeutics.