ATP7B p.Val100fs
c.299_300del · VCV3652123
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Wilson disease
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 21 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.94 | GERP -2.5, phastCons 0.15 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- ATP7B
- Protein
- p.Val100fs
- Coding
- c.299_300del
- MANE Select
- NM_000053
- Type
- Microsatellite
- Location
- chr13:51974920 (GRCh38)
- Gene constraint
- LOEUF 1.063 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 71.83 · 13 PDB
- Residue 100
- the hma 1 domain; a β-strand
Disease context
Wilson disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Wilson disease (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Childhood, Elderly
- Prevalence
- 1-9 / 100 000 (Worldwide)
Similar variants
- ATP7B p.Arg414fs Pathogenic ★★ same condition
- ATP7B p.Ile930del Pathogenic/Likely pathogenic ★★ same condition
- ATP7B p.Leu745fs Pathogenic/Likely pathogenic ★★ same condition
- ATP7B p.Lys1248fs Pathogenic ★★ same condition
- ATP7B p.Val1024fs Pathogenic ★★ same condition
- ATP7B p.Val1187fs Pathogenic/Likely pathogenic ★★ same condition
- ATP7B p.Val883fs Pathogenic ★★ same condition
- ATP7B c.3244-20CT[2] Likely benign ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/atp7b-p-val100fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown