Is LAMA2 p.Pro263= (c.789A>G) pathogenic?

LAMA2 p.Pro263= (c.789A>G) is classified Likely benign in LAMA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-18). Absent from gnomAD v4.1; Associated with LAMA2-related muscular dystrophy.

What condition is associated with LAMA2 p.Pro263= (c.789A>G)?

LAMA2 p.Pro263= (c.789A>G) is associated with LAMA2-related muscular dystrophy (ClinVar).

How common is LAMA2 p.Pro263= (c.789A>G) in the general population?

LAMA2 p.Pro263= (c.789A>G) is absent from gnomAD v4.1 (gnomAD).

LAMA2 p.Pro263=

c.789A>G · rs1778283331 · VCV2786647

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

LAMA2-related muscular dystrophy

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 -1
Overall
CADD	5.859	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: LAMA2
Protein: p.Pro263=
Coding: c.789A>G
MANE Select: NM_000426
dbSNP: rs1778283331
Type: single nucleotide variant
Location: chr6:129144050 (GRCh38)
Gene constraint: LOEUF 0.801 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 263: a UniProt-annotated variant site (in mdc1a); a UniProt-annotated variant site (in lgmdr23); the laminin n-terminal domain

Full LAMA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

LAMA2-related muscular dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LAMA2 c.1028-1G>A Likely pathogenic ★★ same condition
LAMA2 c.112+1G>A Pathogenic/Likely pathogenic ★★ same condition
LAMA2 c.112+2T>C Pathogenic ★★ same condition
LAMA2 c.1467+1G>A Pathogenic/Likely pathogenic ★★ same condition
LAMA2 c.1467+2T>C Pathogenic/Likely pathogenic ★★ same condition
LAMA2 c.1884+1G>A Pathogenic/Likely pathogenic ★★ same condition
LAMA2 c.1884+2T>C Likely pathogenic ★★ same condition
LAMA2 c.1885-1G>A 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/lama2-p-pro263 (accessed [today's date]).

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