LAMP2 p.Val337fs
c.1009del · VCV4952561
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
LAMP2-related disorders
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 8 of 9 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 9.4 | GERP 2.2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- LAMP2
- Protein
- p.Val337fs
- Coding
- c.1009del
- MANE Select
- NM_002294
- Type
- Deletion
- Location
- chrX:120441814 (GRCh38)
- Structure
- AlphaFold pLDDT 83.54 · 2 PDB
- Residue 337
- a disulfide bond; the 'second lumenal domain' region
Disease context
LAMP2-related disorders
Similar variants
- LAMP2 p.Arg266fs Likely pathogenic ★ same condition
- LAMP2 p.Ile279fs Likely pathogenic ★ same condition
- LAMP2 p.Val337Leu Uncertain significance ★ ⚠ same residue
- LAMP2 p.Gln240Ter Pathogenic ★★ same condition
- LAMP2 p.Ser338Ter Pathogenic/Likely pathogenic ★★ same condition
- LAMP2 c.64+5G>C Likely pathogenic ★ same condition
- LAMP2 p.Asp163Ter Likely pathogenic ★ same condition
- LAMP2 p.Lys59Ter 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/lamp2-p-val337fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown