Is LAMP2 p.Phe4= (c.12C>T) pathogenic?

LAMP2 p.Phe4= (c.12C>T) is classified Likely benign in LAMP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-21). Absent from gnomAD v4.1; Associated with LAMP2-related disorder.

What condition is associated with LAMP2 p.Phe4= (c.12C>T)?

LAMP2 p.Phe4= (c.12C>T) is associated with LAMP2-related disorder (ClinVar).

How common is LAMP2 p.Phe4= (c.12C>T) in the general population?

LAMP2 p.Phe4= (c.12C>T) is absent from gnomAD v4.1 (gnomAD).

LAMP2 p.Phe4=

c.12C>T · rs2520948387 · VCV3046646

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

LAMP2-related disorder

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 4	GERP 0.76, phastCons 1
Overall
CADD	12.6	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.Phe4=
Coding: c.12C>T
MANE Select: NM_002294
dbSNP: rs2520948387
Type: single nucleotide variant
Location: chrX:120469158 (GRCh38)
Structure: AlphaFold pLDDT 83.54 · 2 PDB

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

Disease context

LAMP2-related disorder

Similar variants

LAMP2 p.Phe4Leu 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.Lys59Ter Likely pathogenic ★ same condition
LAMP2 p.Ser12Ter Likely pathogenic ★ same condition
LAMP2 p.Val15Leu Uncertain significance ⚠ same condition
LAMP2 c.-8G>C Likely benign 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-phe4 (accessed [today's date]).

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