4p16.3-16.1 deletion
Copy-numberCNV-lossPathogenicCytoplasmic · predictedCNV-loss — Copy-number deletion — 4p16.3-16.1
Gene-level event
Variant Assessment
Therapeutic Implication · CNV-loss
Clinical Evidence
Not observed in ~730k individuals — consistent with a rare allele (ACMG PM2_supporting).
ClinVar classifies this variant as Pathogenic, but does not state what it is classified for. ClinVar records the condition only as "not specified". A classification without a phenotype and an inheritance mode cannot be read as a statement about Wolfram syndrome risk or severity.
- 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★ single submitter. ClinVar "conditions" is the union of all submissions; 0–1★ entries are submitted conditions, not documented phenotypes.
No population breakdown — the variant is absent from gnomAD v4, so no ancestry group has an observed frequency.
No homozygotes — the variant is absent from gnomAD v4 altogether.
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.
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Full Variant Card
4p16.3-16.1 deletion — WFS1 Molecular Atlas Card
Variant type: Copy-number variant (deletion) Region: Chromosome 4p16.3-16.1 (gene-level structural event)
CNV-loss — Copy-number deletion — 4p16.3-16.1
This is a large copy-number deletion spanning 4p16.3-16.1 — a gene-level event causing loss of one copy of this region (wolframin haploinsufficiency or, with a second hit, loss of function). CNVs act by dosage rather than by altering a single residue, so AlphaFold residue mapping, ΔΔG, NMD and AlphaMissense don't apply. Therapeutically these are gene-replacement candidates (restore a working copy); per-residue chaperone/readthrough strategies are not relevant. Confirm breakpoints and gene content against the ClinVar record below.
Clinical evidence
Inheritance and scope
Pathogenic — phenotype scope not stated in ClinVar
ClinVar classifies this variant as Pathogenic, but does not state what it is classified for. ClinVar records the condition only as "not specified". A classification without a phenotype and an inheritance mode cannot be read as a statement about Wolfram syndrome risk or severity.
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.
- Classification: Pathogenic
- Review status: criteria provided, single submitter
- Associated conditions: not specified
- ClinVar accession: VCV004851207
- Genomic variant: GRCh37/hg19 4p16.3-16.1(chr4:68345-11209462)x1
- Last evaluated: 1/01/01 00:00
Card generated by wolfram-atlas-batch (CNV pipeline) on 2026-06-08T03:03:52.326098Z.
CNVs are gene-level events; WFS1 protein reference UniProt O76024 is not residue-mapped here.