Is LAMP2 p.Ala100= (c.300G>C) pathogenic?

LAMP2 p.Ala100= (c.300G>C) is classified Likely benign in LAMP2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-02-03). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with LAMP2 p.Ala100= (c.300G>C)?

LAMP2 p.Ala100= (c.300G>C) is associated with Cardiovascular phenotype, Danon disease (ClinVar).

How common is LAMP2 p.Ala100= (c.300G>C) in the general population?

LAMP2 p.Ala100= (c.300G>C) is absent from gnomAD v4.1 (gnomAD).

LAMP2 p.Ala100=

c.300G>C · rs765548221 · VCV264467

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

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 0.39	GERP -1.1, phastCons 0.99
Overall
CADD	6.634	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: LAMP2
Protein: p.Ala100=
Coding: c.300G>C
MANE Select: NM_002294
dbSNP: rs765548221
Type: single nucleotide variant
Location: chrX:120455454 (GRCh38)
Structure: AlphaFold pLDDT 83.54 · 2 PDB
Residue 100: the 'first lumenal domain' region

Full LAMP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Danon disease

Similar variants

LAMP2 p.Ala100Val Benign/Likely benign ★★ same residue
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

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-ala100 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown