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L554=

SynonymousSilentLikely benignCytoplasmic · predicted
Synonymous variant · codon at position 554 · Lumenal loop 4 · WFS1 (Wolframin)

Silent — Silent — no amino-acid change

Interactive 3D Structure

Interactive structure
rotate · zoom · variant + 5 Å neighbors
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AlphaFold wild-type wolframin · the variant site near residue 554 (Lumenal loop 4) is highlighted.

Variant Assessment

Variant type
Synonymous
Schema
Silent
Silent — no amino-acid change
Domain
Lumenal loop 4
Status
—

Therapeutic Implication · Silent

No amino-acid change (L554 is unchanged): the codon is altered but the protein sequence is identical to wild-type. No structural, stability or AlphaMissense effect applies. Synonymous variants are typically benign unless they affect splicing or regulatory elements; this one is not adjacent to an exon boundary.

Clinical Evidence

ClinVar classificationLikely benign
Review statuscriteria provided, single submitter
Associated conditions—
Population frequency (gnomAD v4)Ultra-rare · AF 0.0025%
cDNA changec.1662G>A
Protein consequenceL554=
ClinVar variantNM_006005.3(WFS1):c.1662G>A (p.Leu554=)
ClinVar accessionVCV001648897
Last evaluated2026/01/26 00:00

Observed at very low frequency in gnomAD.

Therapeutic Strategy Handoff · prediction

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Full Variant Card

L554= — WFS1 Molecular Atlas Card

Variant type: Synonymous (silent) Codon: position 554 (Leucine, L) — amino acid unchanged Domain context: Lumenal loop 4

Schema category: Silent — Silent — no amino-acid change

No amino-acid change (L554 is unchanged): the codon is altered but the protein sequence is identical to wild-type. No structural, stability or AlphaMissense effect applies. Synonymous variants are typically benign unless they affect splicing or regulatory elements; this one is not adjacent to an exon boundary.

Clinical evidence

  • Classification: Likely benign
  • Review status: criteria provided, single submitter
  • cDNA change: c.1662G>A
  • ClinVar accession: VCV001648897
  • Last evaluated: 2026/01/26 00:00
  • Submissions: 1

Card generated by wolfram-atlas-batch (synonymous pipeline) on 2026-06-08T02:54:33.832091Z. WFS1: UniProt O76024, AlphaFold v6. Synonymous variants carry no protein-structural effect.