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L410=

SynonymousSilentLikely benignTransmembrane · predicted
Synonymous variant · codon at position 410 · 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 410 (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 (L410 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, multiple submitters, no conflicts
Associated conditions—
Population frequency (gnomAD v4)Absent from gnomAD v4
cDNA changec.1230C>T
Protein consequenceL410=
ClinVar variantNM_006005.3(WFS1):c.1230C>T (p.Leu410=)
ClinVar accessionVCV002065040
Last evaluated2025/03/30 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

L410= — WFS1 Molecular Atlas Card

Variant type: Synonymous (silent) Codon: position 410 (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 (L410 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, multiple submitters, no conflicts
  • cDNA change: c.1230C>T
  • ClinVar accession: VCV002065040
  • Last evaluated: 2025/03/30 00:00
  • Submissions: 1

Card generated by wolfram-atlas-batch (synonymous pipeline) on 2026-06-08T02:53:06.345304Z. WFS1: UniProt O76024, AlphaFold v6. Synonymous variants carry no protein-structural effect.