A126T

Category 3/4 — Most DruggablePathogenic/Likely pathogenicCytoplasmic · predictedEditorial

Alanine → Threonine at position 126 · N-terminal cytoplasmic domain (87-313) · WFS1 (Wolframin)

An alanine-to-threonine substitution inside wolframin's N-terminal cytoplasmic domain — a region that engages ATP6V1A (the V-ATPase regulatory partner) — and sits adjacent to a free cysteine that adds an unwanted disulfide-formation risk.

Interactive 3D Structure

Wild-type reference

Wild-type A126 — hydrogen bond to L130

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DynaMut2 mutant · A126T

Mutant T126 — hydrogen bond to S123 lost (2 contacts lost)

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Bond changes · DynaMut2 interaction analysis

2 lost4 gained12 preserved

Interaction type	Wild-type partner	Mutant partner	Status
Hydrogen bond	—	L111	Gained
Hydrogen bond	N122	N122	Preserved
Hydrogen bond	S123	—	Lost
Hydrogen bond	—	W129	Gained
Hydrogen bond	L130	L130	Preserved
Polar contact	G107	G107	Preserved
Polar contact	—	L111	Gained
Polar contact	N122	N122	Preserved
Polar contact	S123	S123	Preserved
Polar contact	C124	C124	Preserved
Polar contact	D128	D128	Preserved
Polar contact	W129	W129	Preserved
Polar contact	L130	L130	Preserved
Van der Waals	N122	—	Lost
Van der Waals	C124	C124	Preserved
Van der Waals	D128	D128	Preserved
Van der Waals	—	L130	Gained
Hydrophobic	L111	L111	Preserved

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

-1.76kcal/mol

Destabilising — moderate

AlphaMissense

0.878

LPath

AlphaFold pLDDT

model confidence

Schema

Cat 3/4

Category 3/4 — Most Druggable

Clinical Evidence

ClinVar classificationPathogenic/Likely pathogenic

Review statuscriteria provided, multiple submitters, no conflicts

Associated conditionsWolfram syndrome 1; Optic atrophy

InheritanceBoth autosomal dominant and autosomal recessive inheritance documented.

Population frequency (gnomAD v4)Ultra-rare · AF 0.0018%

cDNA changec.376G>A

ClinVar accessionVCV000372583

Last evaluated2026/01/19 00:00

Observed at very low frequency in gnomAD.

Structural Context

A126 is held between Thr125 (2.45 Angstrom) and Val127 (2.46 Angstrom), with a tight through-space contact cluster: Asn122 (3.70 Angstrom), Ser123 (3.80 Angstrom), Tyr110 (3.85 Angstrom), Gly107 (4.06 Angstrom), Cys124 (4.22 Angstrom), and Asp128 (4.42 Angstrom). The local environment is polar-rich — three threonines and serines, a tyrosine, an aspartate, an asparagine, and a free cysteine within 4.5 Angstrom. This is a well-organized polar interface, almost certainly part of the ATP6V1A-binding surface.

The wild-type alanine's methyl side chain occupies a single non-polar slot in the polar cluster. Threonine adds a hydroxyl and a beta-branched methyl group. The hydroxyl will look for a hydrogen-bond partner — and Asp128 at 4.42 Angstrom, Asn122 at 3.70 Angstrom, and Ser123 at 3.80 Angstrom all qualify. The result is a forced rearrangement of the local hydrogen-bond network: a contact the wild-type kept open (A126 contributed nothing) is now occupied by the threonine hydroxyl, and the polar partners reorganize accordingly.

The Cys124 contact at 4.22 Angstrom is the second mechanistic concern. Free cytoplasmic cysteines are typically reduced, but local hydrogen-bond reorganization can alter the cysteine's pKa or its local solvation, raising the risk of inappropriate disulfide formation under oxidative stress — and ER-stressed cells in Wolfram syndrome are chronically oxidatively stressed. The threonine introduction at 126 thus has two failure modes: direct disruption of the ATP6V1A-binding surface, and secondary destabilization of Cys124 under cellular stress.

DynaMut2 reports DeltaDeltaG = -1.76 kcal/mol — destabilising and the largest magnitude in this batch. AlphaMissense at 0.878 confirms strong functional constraint. The combination of high pLDDT, sizable destabilization, and functional-surface placement makes A126T mechanistically clear.

Amino-acid chemistry

Alanine (small, hydrophobic, methyl side chain) to Threonine (small polar, beta-branched hydroxyl side chain) at position 126. The substitution introduces both a hydroxyl group and beta-branching where the wild-type contributed neither.

Position in the protein

Position 126 sits inside wolframin's N-terminal cytoplasmic domain (residues 87-313), which UniProt explicitly annotates as the Region of interaction with ATP6V1A (V-type proton ATPase catalytic subunit A) — residues 1-321. This is functional regulatory territory. pLDDT 93.0 marks the residue as exceptionally well-modeled.

Druggability Assessment

Final classification: Category 2/3 borderline — pharmacological chaperone with site-directed elements. DeltaDeltaG of -1.76 kcal/mol is at the upper end of the small-magnitude bucket and approaching the chaperone-rescue threshold. The lesion is on a functional surface (ATP6V1A interaction zone), and the disruption is local — both pharmacological chaperone and site-directed small-molecule design are viable approaches. The Cys124 proximity warrants explicit modeling. Any compound designed against this site should be tested for cysteine reactivity, both to confirm no off-target covalent labeling and to verify that it does not inadvertently shift Cys124 toward disulfide-forming geometry. Conversely, antioxidant cofactors that preserve the reduced state of Cys124 may complement chaperone therapy in carriers under oxidative stress.

Why this matters

A126T is the first variant in this batch that sits on an explicitly annotated protein-protein interaction surface — wolframin's contact with ATP6V1A in V-ATPase regulation. Disrupting this interaction has functional consequences distinct from misfolding: it affects wolframin's role as a regulator of cellular acidification and calcium handling, not just its presence at the membrane. The therapeutic implication is that even if A126T-bearing wolframin reaches the membrane in normal abundance, it may functionally underperform. For the Atlas, A126T represents the cytoplasmic-domain Category 3 cluster — where the binding-surface-disruption variants live. These variants demand a different drug-design strategy than the lumenal Cat 3 cluster: stabilizers of the ATP6V1A-wolframin interaction rather than chaperones of wolframin folding alone. Mapping the cluster across the N-terminal cytoplasmic domain is a near-term Atlas deliverable.

Therapeutic Strategy Handoff · prediction

Feed this card to Wolfram Intelligence

Download the A126T 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 A126T PDF card ↓Strategies are AI-generated predictions, not validated therapeutics.

UniProt Domain Annotation

Chain1–890 · Wolframin

Region1–321 · Interaction with ATP6V1A

Natural variant126–126 · in WFS1; dbSNP:rs145639028