G562R

Category 3/4 — Most DruggablePathogenic/Likely pathogenicCytoplasmic · predictedSource card

Glycine → Arginine at position 562 · Lumenal loop 4 · WFS1 (Wolframin)

Interactive 3D Structure

Wild-type reference

Wild-type G562 — hydrogen bond to R558

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DynaMut2 mutant · G562R

Mutant R562 — carbonyl to A559 lost (2 contacts lost)

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Bond changes · DynaMut2 interaction analysis

2 lost0 gained9 preserved

Interaction type	Wild-type partner	Mutant partner	Status
Hydrogen bond	R558	R558	Preserved
Hydrogen bond	A559	A559	Preserved
Hydrogen bond	F566	F566	Preserved
Polar contact	R558	R558	Preserved
Polar contact	A559	A559	Preserved
Polar contact	S560	S560	Preserved
Polar contact	F566	F566	Preserved
Carbonyl	A559	—	Lost
Van der Waals	A559	A559	Preserved
Van der Waals	S560	S560	Preserved
Van der Waals	F566	—	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

-0.42kcal/mol

Destabilising — mild

AlphaMissense

0.991

likely pathogenic

AlphaFold pLDDT

model confidence

Schema

Cat 3/4

Category 3/4 — Most Druggable

Clinical Evidence

ClinVar classificationLikely pathogenic/Likely risk allele

Review statuscriteria provided, multiple submitters, no conflicts

Associated conditionsWolfram syndrome 1

Population frequency (gnomAD v4)Absent from gnomAD v4

cDNA changec.1684G>C

ClinVar accessionVCV000215392

Last evaluated2016/09/28 00:00

Not observed in ~730k individuals — consistent with a rare allele (ACMG PM2_supporting).

Full Variant Card

WFS1 Wolframin — G562R Variant Card

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

Glycine → Arginine at position 562. Lumenal loop 4. ClinVar Likely pathogenic/Likely risk allele, AlphaMissense 0.991, DynaMut2 ΔΔG -0.42 kcal/mol (destabilising).

Identity

Field	Value
Variant	G562R (p.Glycine562Arginine)
DNA change	c.1684G>C
Gene · Protein	WFS1 · Wolframin (890 aa)
UniProt	O76024 · WFS1_HUMAN
ClinVar accession	VCV000215392
Amino acid change	Glycine (G) → Arginine (R)

Structural Context

Field	Value
AlphaFold model	AF-O76024-F1, v6
pLDDT at residue 562	82.56 — well-folded
Domain	Lumenal loop 4
Position context	C-terminal lumenal domain · position 562 projects into the ER lumen
IDR flag	No — pLDDT above 50 threshold

UniProt features at this position:

(none catalogued)

Position 562 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 positively charged (arginine — guanidinium, strong H-bond donor). The chemistry shift implies altered local packing, hydrogen-bonding, and/or electrostatics at this site.

Computational Predictions

AlphaMissense

Field	Value
am_pathogenicity	0.9909
am_class	likely pathogenic
Interpretation	Likely pathogenic (threshold 0.564)

DynaMut2

Field	Value
ΔΔG (kcal/mol)	-0.42 (Destabilising)
Job ID	178094554518
Result URL	https://biosig.lab.uq.edu.au/dynamut2/results_prediction/178094554518

Clinical Evidence

Field	Value
Classification	Likely pathogenic/Likely risk allele
Review status	criteria provided, multiple submitters, no conflicts
Last evaluated	2016/09/28 00:00
Inheritance	Autosomal recessive Wolfram syndrome 1 phenotype documented.
WFS1 variant landscape	G562R is 1 of ~326 pathogenic-spectrum variants in WFS1 (out of 2,243 catalogued in ClinVar)

Wolfram syndrome 1

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|=0.42 < 2 kcal/mol (fold intact) + AlphaMissense 0.991 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|=0.42 kcal/mol). The pathogenic signal is real — AlphaMissense places it at 0.991. 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
G562R_molstar_viewer.html — interactive 3D viewer (auto-highlights position 562 with ball-and-stick + neighbors within 5Å)
G562R_variant_card.md — this card (source of truth)
G562R_variant_card.html — styled printable card
G562R_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)
G562R_wildtype_interactions.pse / G562R_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 G562R 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 G562R PDF card ↓Strategies are AI-generated predictions, not validated therapeutics.