LAMP2 p.Ser277=
c.831C>T · VCV3866393
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00146%, nfe)
Conditions
2
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.5 | GERP 0.13, phastCons 1 |
| Overall | ||
| CADD | 8.856 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00146%
European (non-Finnish) · 13/888,341 alleles
Filtering AF
0.000816%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000629%
Overall
0.00119%
13/1,090,377 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- LAMP2
- Protein
- p.Ser277=
- Coding
- c.831C>T
- MANE Select
- NM_002294
- Type
- single nucleotide variant
- Location
- chrX:120446338 (GRCh38)
- Structure
- AlphaFold pLDDT 83.54 · 2 PDB
- Residue 277
- the 'second lumenal domain' region
Similar variants
- LAMP2 c.1093+1G>A Pathogenic ★★ same condition
- LAMP2 c.183+1G>A Pathogenic/Likely pathogenic ★★ same condition
- LAMP2 c.183+2T>C Pathogenic ★★ same condition
- LAMP2 c.65-1G>C Pathogenic/Likely pathogenic ★★ same condition
- LAMP2 c.65-2A>G Pathogenic ★★ same condition
- LAMP2 c.741+1G>A Pathogenic/Likely pathogenic ★★ same condition
- LAMP2 c.864+1G>A Pathogenic ★★ same condition
- LAMP2 c.864+1G>T Pathogenic/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-ser277 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown