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L409=

SynonymousSilentLikely benignTransmembrane · predicted
Synonymous variant · codon at position 409 · Transmembrane helix 4 · WFS1 (Wolframin)

Silent — Silent — but near an exon boundary (splice effect possible)

Interactive 3D Structure

Interactive structure
rotate · zoom · variant + 5 Å neighbors
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AlphaFold wild-type wolframin · the variant site near residue 409 (Transmembrane helix 4) is highlighted.

Variant Assessment

Variant type
Synonymous
Schema
Silent
Silent — but near an exon boundary (splice effect possible)
Domain
Transmembrane helix 4
Status
—

Therapeutic Implication · Silent

No amino-acid change (L409 is unchanged), so there is no protein-level structural or stability effect. However, this codon sits within 3 residues of the exon junction near protein position 412 — close enough that the nucleotide change could perturb splicing. Worth a SpliceAI check (Wave 2); otherwise expected to be benign at the protein level.

Clinical Evidence

ClinVar classificationLikely benign
Review statuscriteria provided, single submitter
Associated conditions—
Population frequency (gnomAD v4)Absent from gnomAD v4
cDNA changec.1227G>A
Protein consequenceL409=
ClinVar variantNM_006005.3(WFS1):c.1227G>A (p.Leu409=)
ClinVar accessionVCV001910589
Last evaluated2022/09/13 00:00

Not observed in ~730k individuals — consistent with a rare allele (ACMG PM2_supporting).

Therapeutic Strategy Handoff · prediction

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Full Variant Card

L409= — WFS1 Molecular Atlas Card

Variant type: Synonymous (silent) Codon: position 409 (Leucine, L) — amino acid unchanged Domain context: Transmembrane helix 4

Schema category: Silent — Silent — but near an exon boundary (splice effect possible)

No amino-acid change (L409 is unchanged), so there is no protein-level structural or stability effect. However, this codon sits within 3 residues of the exon junction near protein position 412 — close enough that the nucleotide change could perturb splicing. Worth a SpliceAI check (Wave 2); otherwise expected to be benign at the protein level.

Clinical evidence

  • Classification: Likely benign
  • Review status: criteria provided, single submitter
  • cDNA change: c.1227G>A
  • ClinVar accession: VCV001910589
  • Last evaluated: 2022/09/13 00:00
  • Submissions: 1

Card generated by wolfram-atlas-batch (synonymous pipeline) on 2026-06-08T02:53:04.726566Z. WFS1: UniProt O76024, AlphaFold v6. Synonymous variants carry no protein-structural effect.