A433P

Category 3/4 — Most DruggableLikely pathogenicTransmembrane · predictedEditorial

Alanine → Proline at position 433 · TM4 (427-447), helical transmembrane · WFS1 (Wolframin)

Alanine-to-proline mutation inside transmembrane helix TM4 — a classical helix-breaking substitution that introduces a backbone kink into a structural element that must remain alpha-helical to function as a membrane anchor.

Interactive 3D Structure

Wild-type reference

Wild-type A433 — hydrogen bond to T436

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DynaMut2 mutant · A433P

Mutant P433 — hydrogen bond to C429 lost (2 contacts lost)

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Bond changes · DynaMut2 interaction analysis

2 lost1 gained10 preserved

Interaction type	Wild-type partner	Mutant partner	Status
Hydrogen bond	C429	C429	Preserved
Hydrogen bond	T436	T436	Preserved
Hydrogen bond	G437	G437	Preserved
Polar contact	C429	C429	Preserved
Polar contact	—	S430	Gained
Polar contact	E431	—	Lost
Polar contact	T436	T436	Preserved
Polar contact	G437	G437	Preserved
Van der Waals	C429	C429	Preserved
Van der Waals	E431	—	Lost
Van der Waals	T436	T436	Preserved
Hydrophobic	I547	I547	Preserved
Hydrophobic	L556	L556	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

-0.05kcal/mol

Destabilising — mild

AlphaMissense

0.990

LPath

AlphaFold pLDDT

model confidence

Schema

Cat 3/4

Category 3/4 — Most Druggable

Clinical Evidence

ClinVar classificationLikely pathogenic

Review statusno assertion criteria provided

Associated conditionsOptic atrophy

InheritanceInheritance pattern documented: optic atrophy.

Population frequency (gnomAD v4)Ultra-rare · AF 0.000068%

cDNA changec.1297G>C

ClinVar accessionVCV003250063

Last evaluated2019/01/01 00:00

Observed at very low frequency in gnomAD.

Structural Context

A433 is held between Val434 (2.47 Angstrom) and Leu432 (2.48 Angstrom), with through-space contacts to Thr436 (3.30 Angstrom), Cys429 (3.61 Angstrom), Ile547 (4.04 Angstrom — note: this is far in sequence, indicating an inter-helix contact, likely with TM5), Ser430 (4.10 Angstrom), Glu431 (4.35 Angstrom), and Ile435 (4.42 Angstrom). The contact set tells two stories: a hydrophobic packing core within TM4 itself (Val434, Leu432, Ile435), and an inter-helix interaction with TM5 (Ile547 at 4.04 Angstrom). The wild-type alanine's compact methyl fits cleanly into both contexts.

The Cys429 contact at 3.61 Angstrom is mechanistically important. A free cysteine inside a transmembrane helix at close distance to A433 suggests the wild-type geometry holds the cysteine in a defined orientation. If A433P perturbs that geometry, the cysteine's local environment changes — and a TM-buried cysteine that becomes solvent-accessible or shifts toward an oxidative environment becomes a disulfide-formation liability.

Replacing A433 with proline is one of the most disruptive single-residue substitutions possible inside an alpha-helix. Proline's pyrrolidine ring forces phi near -60 degrees (incompatible with the standard alpha-helix phi of -60 to -65 degrees only when its other constraints are also satisfied — typically not in the middle of an extended helix) and eliminates the backbone amide NH needed for the i-to-i+4 hydrogen bond that defines the alpha-helix structure. Proline insertions in the middle of TM helices reliably introduce 20-30 degree kinks in the helix axis.

The consequence for TM4 is a kink at residue 433 that propagates upward and downward through the helix, shifting the inter-helix register with TM5 (the Ile547 contact at 4.04 Angstrom). The Cys429 environment is also disturbed.

DynaMut2 reports DeltaDeltaG = -0.05 kcal/mol — essentially zero. This is a known limitation of energy functions for proline introductions: the local van der Waals improvement from proline's rigid ring partially compensates the lost hydrogen-bonding capacity, and the energy function under-weighs the structural propagation cost. AlphaMissense at 0.990 reads the true severity: A433P is essentially a TM4 disruption, predicted to be near-fully pathogenic.

Amino-acid chemistry

Alanine (small, hydrophobic, helix-promoting — alanine has one of the highest alpha-helix propensities of any amino acid) to Proline (cyclic side chain, locks backbone phi near -60 degrees, lacks the amide NH needed for the alpha-helix hydrogen-bond network, the canonical helix-breaker) at position 433.

Position in the protein

Position 433 sits inside transmembrane helix TM4 (residues 427-447) — one of wolframin's eleven membrane-spanning helices. The residue is buried in the ER bilayer interior and contributes to inter-helix packing. pLDDT 91.31 confirms a confidently modeled position.

Druggability Assessment

Final classification: Category 3 — Most Druggable per the schema's DeltaDeltaG-magnitude rule, but with a strong structural-chemistry override note. A proline introduction in a TM helix is mechanistically severe regardless of what the energy function reports. The variant likely behaves more like Category 2 (chaperone-rescuable) or even Category 1 (gene therapy candidate) in practice, depending on how cleanly TM4 inserts into the bilayer with the proline-induced kink. For druggability, pharmacological chaperones that stabilize TM4 packing during co-translational membrane insertion are the most plausible therapeutic route. The Cys429 disulfide-formation risk should be modeled explicitly. Site-directed compound design against TM4 from the lumenal or cytoplasmic face is challenging given the buried geometry, but the helix-helix interface with TM5 (the Ile547 contact) is a potential anchor for stabilizing molecules.

Why this matters

A433P is the second buried-TM proline introduction in the Atlas batch this week (alongside A806P, which is in the lumenal domain rather than a TM helix). The Atlas's treatment of TM proline introductions is a recurring pattern: the energy function under-reads, AlphaMissense correctly flags, and the structural chemistry argues for an override to a more serious category. This pattern matters because TM helix mutations are mechanistically tractable in a way the lumenal-domain mutations are not — pharmacological chaperone screening has a long history of rescuing TM-folding defects in proteins like CFTR, rhodopsin, and the V2 vasopressin receptor. If the wolframin program adopts the same chaperone-screening strategy, TM helix variants like A433P and G437R are the highest-priority candidates.

Therapeutic Strategy Handoff · prediction

Feed this card to Wolfram Intelligence

Download the A433P 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 A433P PDF card ↓Strategies are AI-generated predictions, not validated therapeutics.

UniProt Domain Annotation

Chain1–890 · Wolframin

Transmembrane427–447 · Helical