PTCH1 p.Lys89fs
c.267del · VCV3776311
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
basal cell nevus syndrome 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 24 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 9.4 | GERP 1.7, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PTCH1
- Protein
- p.Lys89fs
- Coding
- c.267del
- MANE Select
- NM_000264
- Type
- Deletion
- Location
- chr9:95506534 (GRCh38)
- Gene constraint
- LOEUF 0.146 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 74.36 · 16 PDB
- Residue 89
- an α-helix; the 'pre-tm1' region
Similar variants
- PTCH1 p.Lys370fs Pathogenic/Likely pathogenic ★★ same condition
- PTCH1 p.Pro253fs Pathogenic/Likely pathogenic ★★ same condition
- PTCH1 p.Lys89Arg Uncertain significance ★★ ⚠ same residue
- PTCH1 p.Lys89Asn Uncertain significance ★★ ⚠ same residue
- PTCH1 c.1602+15_1602+17del Benign/Likely benign ★★ same condition
- PTCH1 p.Arg1336fs Likely pathogenic ★ same condition
- PTCH1 p.Glu1120fs Likely pathogenic ★ same condition
- PTCH1 p.Glu279fs Likely pathogenic ★ 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/ptch1-p-lys89fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown