R653C
Category 4 — Stable Fold, Function DisruptedConflictingLumenal · predictedσ-1 candidateEditorialArginine → Cysteine at position 653 in lumenal domain. ClinVar Conflicting. AlphaMissense 0.476 (below threshold), ΔΔG +0.22. pLDDT 61 borderline.
Interactive 3D Structure
Bond changes · DynaMut2 interaction analysis
| Interaction type | Wild-type partner | Mutant partner | Status |
|---|---|---|---|
| Hydrogen bond | F649 | F649 | Preserved |
| Hydrogen bond | Y650 | Y650 | Preserved |
| Hydrogen bond | G656 | G656 | Preserved |
| Polar contact | F649 | F649 | Preserved |
| Polar contact | Y650 | Y650 | Preserved |
| Polar contact | V651 | V651 | Preserved |
| Polar contact | G656 | G656 | Preserved |
| Van der Waals | — | Y650 | Gained |
| Van der Waals | V651 | V651 | Preserved |
| Van der Waals | E655 | E655 | Preserved |
| Hydrophobic | F649 | — | 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
- pLDDT 61.31 below 70
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 in the general population.
ClinVar classifies this variant as Conflicting classifications of pathogenicity for WFS1-related spectrum (unresolved mode) (dominant or recessive); Nonsyndromic hearing loss (DFNA6/14/38) (autosomal dominant, OMIM 600965); WFS1-related diabetes (autosomal dominant); Wolfram syndrome (classic) (autosomal recessive, OMIM 222300); Cataract 41 (autosomal dominant, OMIM 116400); Wolfram-like syndrome (autosomal dominant, OMIM 614296); Retinal dystrophy (inheritance not specified). ClinVar records this under a WFS1-spectrum label that spans both disease families — recessive Wolfram syndrome (biallelic) and the dominant WFS1-related disorders. The label does not resolve which applies, and it is not a severity statement.
- WFS1-related spectrum (unresolved mode)dominant or recessivesubmitted as: WFS1-Related Spectrum Disorders
- Nonsyndromic hearing loss (DFNA6/14/38)autosomal dominant · OMIM 600965submitted as: Autosomal dominant nonsyndromic hearing loss 6; Autosomal dominant nonsyndromic hearing loss 6
- WFS1-related diabetesautosomal dominantsubmitted as: Type 2 diabetes mellitus
- Wolfram syndrome (classic)autosomal recessive · OMIM 222300submitted as: Wolfram syndrome 1
- Cataract 41autosomal dominant · OMIM 116400submitted as: Cataract 41
- Wolfram-like syndromeautosomal dominant · OMIM 614296submitted as: Wolfram-like syndrome
- Retinal dystrophyinheritance not specifiedsubmitted as: Retinal dystrophy
- 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 Ashkenazi Jewish: AF 0.557% (165 of 29,608 alleles), 19.7x the global figure. The global AF describes the general population, not the at-risk group.
2 homozygotes reported in gnomAD v4 (1 Ashkenazi Jewish; 1 Admixed American). gnomAD excludes individuals with severe pediatric disease, so homozygotes in this dataset argue against a fully penetrant severe recessive phenotype and belong in the clinical picture. This is interpretive signal, not a classification.
| Ancestry group | Allele freq. | AC / AN | Hom. | Carrier est. |
|---|---|---|---|---|
| Ashkenazi Jewish | 0.557% | 165 / 29,608 | 1 | ~1 in 90 |
| Admixed American | 0.183% | 110 / 60,032 | 1 | ~1 in 270 |
| East Asian | 0.085% | 38 / 44,874 | 0 | ~1 in 590 |
| Remaining individuals | 0.062% | 39 / 62,506 | 0 | ~1 in 800 |
| South Asian | 0.016% | 15 / 91,090 | 0 | ~1 in 3040 |
| European (non-Finnish) | 0.0072% | 85 / 1,180,024 | 0 | ~1 in 6940 |
| African / African American | 0.0053% | 4 / 75,058 | 0 | ~1 in 9380 |
| Finnish · under-sampled | 0.0016% | 1 / 63,664 | 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 653 at the lumenal domain start. Neighbors: SER654 (2.5 Å), TYR652 (2.5 Å), TYR650 (3.6 Å — Y650H/Y650D/Y650C region!), PHE649 (3.8 Å — Y650 cluster).
R653C sits adjacent to the Y650 aromatic cluster (multiple Atlas variants at Y650). The introduced thiol could engage in aberrant disulfide chemistry. AM 0.476 below threshold but multi-phenotype + ClinVar Pathogenic raise concern.
Druggability Assessment
Mechanism: charge loss + thiol near Y650 cluster. Therapeutic: same Y650 microregion. Wet-lab validation recommended.
Why this matters
Feed this card to Wolfram Intelligence
Download the R653C 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.