I416N

Category 3/4 — Most DruggableUncertain significanceTransmembrane · predictedSource card

Isoleucine → Asparagine at position 416 · Transmembrane helix 4 · WFS1 (Wolframin)

Interactive 3D Structure

Wild-type reference

Wild-type I416 — hydrogen bond to V412

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DynaMut2 mutant · I416N

Mutant N416 — polar contact to V412 lost (9 contacts lost)

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Bond changes · DynaMut2 interaction analysis

9 lost2 gained5 preserved

Interaction type	Wild-type partner	Mutant partner	Status
Hydrogen bond	V412	V412	Preserved
Hydrogen bond	—	F413	Gained
Polar contact	V412	V412	Preserved
Polar contact	F413	F413	Preserved
Polar contact	P420	P420	Preserved
Polar contact	F877	F877	Preserved
Polar contact	—	F881	Gained
Van der Waals	V412	—	Lost
Van der Waals	F881	—	Lost
Van der Waals	F882	—	Lost
Hydrophobic	V412	—	Lost
Hydrophobic	M539	—	Lost
Hydrophobic	F877	—	Lost
Hydrophobic	A878	—	Lost
Hydrophobic	F881	—	Lost
Hydrophobic	F882	—	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

-1.79kcal/mol

Destabilising — moderate

AlphaMissense

0.934

likely pathogenic

AlphaFold pLDDT

model confidence

Schema

Cat 3/4

Category 3/4 — Most Druggable

Clinical Evidence

ClinVar classificationUncertain significance

Review statuscriteria provided, single submitter

Associated conditions—

Population frequency (gnomAD v4)Ultra-rare · AF 0.00066%

cDNA changec.1247T>A

ClinVar accessionVCV004746132

Last evaluated2025/05/27 00:00

Observed at very low frequency in gnomAD.

Full Variant Card

WFS1 Wolframin — I416N Variant Card

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

Isoleucine → Asparagine at position 416. Transmembrane helix 4. ClinVar Uncertain significance, AlphaMissense 0.934, DynaMut2 ΔΔG -1.79 kcal/mol (destabilising).

Identity

Field	Value
Variant	I416N (p.Isoleucine416Asparagine)
DNA change	c.1247T>A
Gene · Protein	WFS1 · Wolframin (890 aa)
UniProt	O76024 · WFS1_HUMAN
ClinVar accession	VCV004746132
Amino acid change	Isoleucine (I) → Asparagine (N)

Structural Context

Field	Value
AlphaFold model	AF-O76024-F1, v6
pLDDT at residue 416	91.19 — well-folded
Domain	Transmembrane helix 4
Position context	Inside Transmembrane helix 4 · position 416 is bilayer-embedded
IDR flag	No — pLDDT above 50 threshold

UniProt features at this position:

(none catalogued)

Position 416 sits in a transmembrane helix (Transmembrane helix 4). 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 medium hydrophobic (isoleucine — branched); 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	0.9345
am_class	likely pathogenic
Interpretation	Likely pathogenic (threshold 0.564)

DynaMut2

Field	Value
ΔΔG (kcal/mol)	-1.79 (Destabilising)
Job ID	178092102279
Result URL	https://biosig.lab.uq.edu.au/dynamut2/results_prediction/178092102279

Clinical Evidence

Field	Value
Classification	Uncertain significance
Review status	criteria provided, single submitter
Last evaluated	2025/05/27 00:00
Inheritance	Inheritance pattern not specified in ClinVar entry; WFS1 has both AD and AR presentations.
WFS1 variant landscape	I416N 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 3/4 — Most Druggable

<strong>Category 3/4 — Most Druggable</strong><br/><br/>|ΔΔG|=1.79 < 2 kcal/mol (fold intact) + AlphaMissense 0.934 confirms functional impact. Specific local contacts disrupted — priority for docking and pharmacological chaperone screening.

Why this card matters. Wolframin's fold survives this substitution (|ΔΔG|=1.79 kcal/mol). The pathogenic signal is real — AlphaMissense places it at 0.934. 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
I416N_molstar_viewer.html — interactive 3D viewer (auto-highlights position 416 with ball-and-stick + neighbors within 5Å)
I416N_variant_card.md — this card (source of truth)
I416N_variant_card.html — styled printable card
I416N_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)
I416N_wildtype_interactions.pse / I416N_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 I416N 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 I416N PDF card ↓Strategies are AI-generated predictions, not validated therapeutics.