P607L
Category 4 — Stable Fold, Function DisruptedConflictingTransmembrane · predictedEditorialProline → Leucine at position 607 inside TM9. ClinVar Conflicting including monogenic diabetes, T2D, DFNA6. AlphaMissense 0.416 (below threshold), ΔΔG -0.27. Same position as P607R — proline-removal pair.
Interactive 3D Structure
Bond changes · DynaMut2 interaction analysis
| Interaction type | Wild-type partner | Mutant partner | Status |
|---|---|---|---|
| Hydrogen bond | C604 | — | Lost |
| Hydrogen bond | L610 | L610 | Preserved |
| Hydrogen bond | R611 | R611 | Preserved |
| Polar contact | V603 | — | Lost |
| Polar contact | C604 | — | Lost |
| Polar contact | L610 | L610 | Preserved |
| Polar contact | R611 | R611 | Preserved |
| Van der Waals | R611 | — | Lost |
| Hydrophobic | — | L610 | 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
- pLDDT 65.88 below 70
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.
The underlying AlphaFold model has pLDDT below 70 at this position, so the structure the stability calculation was run on is itself uncertain.
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 WFS1-related diabetes (autosomal dominant); Nonsyndromic hearing loss (DFNA6/14/38) (autosomal dominant, OMIM 600965); Wolfram-like syndrome (autosomal dominant, OMIM 614296); Cataract 41 (autosomal dominant, OMIM 116400); Wolfram syndrome (classic) (autosomal recessive, OMIM 222300). These are two clinically distinct disease families: classic Wolfram syndrome requires two affected copies, while the dominant WFS1-related disorders do not. One label covers both, and it does not tell you which applies to a given person.
- WFS1-related diabetesautosomal dominantsubmitted as: Monogenic diabetes; Type 2 diabetes mellitus
- Nonsyndromic hearing loss (DFNA6/14/38)autosomal dominant · OMIM 600965submitted as: Autosomal dominant nonsyndromic hearing loss 6
- Wolfram-like syndromeautosomal dominant · OMIM 614296submitted as: Wolfram-like syndrome
- Cataract 41autosomal dominant · OMIM 116400submitted as: Cataract 41
- 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 African / African American: AF 0.021% (16 of 75,060 alleles), 10.1x 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. |
|---|---|---|---|---|
| African / African American | 0.021% | 16 / 75,060 | 0 | ~1 in 2350 |
| East Asian | 0.018% | 8 / 44,860 | 0 | ~1 in 2800 |
| Remaining individuals | 0.0048% | 3 / 62,504 | 0 | ~1 in 10420 |
| European (non-Finnish) | 0.00059% | 7 / 1,180,014 | 0 | ~1 in 84290 |
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 607 same neighbors as P607R: LEU608 (2.5 Å), VAL606 (2.5 Å), LEU610 (4.1 Å), SER605 (4.5 Å).
P607L is the second pathogenic substitution at 607 (with P607R). Both remove the wild-type proline kink at TM9's end. P607L is the conservative hydrophobic substitution; P607R adds charge.
AM 0.416 below threshold and multi-phenotype does not resolve it (ClinVar: conflicting submissions).
Druggability Assessment
Mechanism: same TM9 kink-removal as P607R. Therapeutic: TM9 site-directed.
Why this matters
Feed this card to Wolfram Intelligence
Download the P607L 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.