S430L
Category 3/4 — Most DruggableConflictingTransmembrane · predictedEditorialSerine → Leucine at position 430 inside TM4. ClinVar Conflicting including Wolfram syndrome 1. AlphaMissense 0.932, ΔΔG -0.01 (neutral). Same position as S430W (Atlas card adjacent).
Interactive 3D Structure
Bond changes · DynaMut2 interaction analysis
| Interaction type | Wild-type partner | Mutant partner | Status |
|---|---|---|---|
| Hydrogen bond | — | A433 | Gained |
| Hydrogen bond | V434 | V434 | Preserved |
| Hydrogen bond | G555 | — | Lost |
| Polar contact | P428 | P428 | Preserved |
| Polar contact | V434 | V434 | Preserved |
| Polar contact | — | G555 | Gained |
| Polar contact | A559 | — | Lost |
| Van der Waals | P428 | P428 | Preserved |
| Hydrophobic | — | P428 | Gained |
| Hydrophobic | — | A559 | 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
- transmembrane position; predictor benchmarked on soluble proteins
This variant sits in the transmembrane band. The stability value was computed with a predictor benchmarked on water-soluble proteins. Published benchmarks of ddG predictors on membrane proteins report correlation below 0.4. Treat the magnitude as unreliable and the sign as weak evidence only.
Do not rank this value against a variant from a different region on ΔΔG alone.
Clinical Evidence
Observed at very low frequency in gnomAD.
ClinVar classifies this variant as Conflicting classifications of pathogenicity for Wolfram syndrome (classic) (autosomal recessive, OMIM 222300). Classic Wolfram syndrome is recessive: a single copy does not produce it, and this classification says nothing about a carrier's own risk.
- Wolfram syndrome (classic)autosomal recessive · OMIM 222300submitted as: Wolfram syndrome 1
- Submitters conflict on this classification (1★). Treat the conditions above as submitted, not as documented phenotypes.
- Phenotype scope is interpretation of submitted records. The computed values on this card (AlphaMissense, DynaMut2 ΔΔG, pLDDT) are measurements of the model, not of a patient.
- Presentation cannot be generalised from neighbouring variants: one nucleotide over can present very differently. Structural similarity supports a mechanistic hypothesis, never a phenotype claim.
Review status: 1★ conflicting classifications. ClinVar "conditions" is the union of all submissions; 0–1★ entries are submitted conditions, not documented phenotypes.
Highest in East Asian: AF 0.0089% (4 of 44,884 alleles), 3.5x the global figure. The global AF describes the general population, not the at-risk group.
No homozygotes reported in gnomAD v4. For a recessive allele this is expected and is not, on its own, evidence either way.
| Ancestry group | Allele freq. | AC / AN | Hom. | Carrier est. |
|---|---|---|---|---|
| East Asian | 0.0089% | 4 / 44,884 | 0 | ~1 in 5610 |
| European (non-Finnish) | 0.0031% | 36 / 1,180,032 | 0 | ~1 in 16390 |
| South Asian · under-sampled | 0.0011% | 1 / 91,088 | 0 | — |
Source: gnomAD r4, retrieved 2026-08-21. Values are allele frequencies. The carrier estimate is derived from the allele frequency (Hardy-Weinberg, ~2·AF) and is an approximation, not a published figure — where a published carrier frequency exists it outranks this column and is cited on the card.
Structural Context
Position 430 sits in TM4 with the E431 hub contact. Same neighbors as S430W: CYS429 (2.5 Å), GLU431 (2.5 Å — E431 hub), SER551 (4.0 Å — TM4-TM7 cross-helix), PRO428 (4.1 Å), ALA433 (4.4 Å).
S430L is the second substitution at position 430 (with S430W). Where S430W introduced massive aromatic volume, S430L introduces conservative aliphatic volume. The H-bond between S430's hydroxyl and E431's carboxylate is lost in both — same mechanism.
The near-zero ΔΔG indicates fold easily accommodates the more conservative leucine. AlphaMissense 0.932 + Wolfram 1 confirm severe functional consequence.
Druggability Assessment
Mechanism: loss of S430-E431 H-bond. Therapeutic: same E431 hub target as S430W.
Why this matters
Feed this card to Wolfram Intelligence
Download the S430L 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.