Is LAMC2 p.Arg533= (c.1599G>C) pathogenic?

LAMC2 p.Arg533= (c.1599G>C) is classified Likely benign in LAMC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-23). Absent from gnomAD v4.1.

How common is LAMC2 p.Arg533= (c.1599G>C) in the general population?

LAMC2 p.Arg533= (c.1599G>C) is absent from gnomAD v4.1 (gnomAD).

LAMC2 p.Arg533=

c.1599G>C · rs2526070041 · VCV2808533

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 0.21	GERP -2.6
Overall
CADD	7.905	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: LAMC2
Protein: p.Arg533=
Coding: c.1599G>C
MANE Select: NM_005562
dbSNP: rs2526070041
Type: single nucleotide variant
Location: chr1:183228504 (GRCh38)
Gene constraint: LOEUF 0.797 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 72.89
Residue 533: the laminin egf-like 7 domain

Full LAMC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

LAMC2 p.Arg533Gln Uncertain significance ★ ⚠ same residue
LAMC2 p.Arg533Pro Uncertain significance ★ ⚠ same residue
LAMC2 p.Arg533Trp Uncertain significance ★ ⚠ same residue
LAMC2 p.Arg533fs Pathogenic ★ same residue
LAMC2 c.1715-2A>G Likely pathogenic ★★ same type
LAMC2 c.268+1G>A Likely pathogenic ★★ same type
LAMC2 c.3328+1G>A Pathogenic/Likely pathogenic ★★ same type
LAMC2 c.640+1G>A Likely pathogenic ★★ same type

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/lamc2-p-arg533 (accessed [today's date]).

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