ATP7B p.Thr99fs
c.294del · VCV4085353
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
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 -0.61 | GERP -5.2 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- ATP7B
- Protein
- p.Thr99fs
- Coding
- c.294del
- MANE Select
- NM_000053
- Type
- Deletion
- Location
- chr13:51974926 (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 99
- the hma 1 domain; a β-strand
Similar variants
- ATP7B p.Thr99Pro Uncertain significance ★ ⚠ same residue
- ATP7B c.1700_1707+16del Likely pathogenic ★★ same type
- ATP7B c.1705_1707+10del Pathogenic ★★ same type
- ATP7B c.2866-2del Pathogenic/Likely pathogenic ★★ same type
- ATP7B c.3700del Pathogenic ★★ same type
- ATP7B c.3904-2del Pathogenic/Likely pathogenic ★★ same type
- ATP7B c.-436_-422del Pathogenic ★★ same type
- ATP7B p.Ala1135fs Pathogenic ★★ same type
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-thr99fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown