Is LAMP2 p.Arg53= (c.159C>T) pathogenic?

LAMP2 p.Arg53= (c.159C>T) is classified Likely benign in LAMP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-27). No allele count reported in gnomAD v4.1 (AN 1,146,808); Associated with Cardiovascular phenotype.

What condition is associated with LAMP2 p.Arg53= (c.159C>T)?

LAMP2 p.Arg53= (c.159C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is LAMP2 p.Arg53= (c.159C>T) in the general population?

LAMP2 p.Arg53= (c.159C>T) is no allele count reported in gnomAD v4.1 (AN 1,146,808) (gnomAD).

LAMP2 p.Arg53=

c.159C>T · VCV3866394

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,146,808)

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 -2.5	GERP -3.3
Overall
CADD	1.114	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,146,808). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: LAMP2
Protein: p.Arg53=
Coding: c.159C>T
MANE Select: NM_002294
Type: single nucleotide variant
Location: chrX:120456675 (GRCh38)
Structure: AlphaFold pLDDT 83.54 · 2 PDB
Residue 53: 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

Similar variants

LAMP2 p.Arg53His Conflicting classifications of pathogenicity ★ ⚠ same residue
LAMP2 p.Arg53Cys Benign/Likely benign ★★ ⚠ same residue
LAMP2 p.Arg53Leu Uncertain significance ★ ⚠ same residue
LAMP2 c.183+1G>A Pathogenic/Likely pathogenic ★★ same condition
LAMP2 c.741+1G>A Pathogenic/Likely pathogenic ★★ same condition
LAMP2 p.Cys232Ter Pathogenic ★★ same condition
LAMP2 p.Gln359Ter Pathogenic/Likely pathogenic ★★ same condition
LAMP2 p.Met1Leu 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-arg53 (accessed [today's date]).

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