Is LAMA2 p.Phe397fs (c.1188dup) pathogenic?

LAMA2 p.Phe397fs (c.1188dup) is classified Likely pathogenic in LAMA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-09). No gnomAD frequency available for this variant; Associated with congenital merosin-deficient muscular dystrophy 1A.

What condition is associated with LAMA2 p.Phe397fs (c.1188dup)?

LAMA2 p.Phe397fs (c.1188dup) is associated with congenital merosin-deficient muscular dystrophy 1A (ClinVar).

How common is LAMA2 p.Phe397fs (c.1188dup) in the general population?

LAMA2 p.Phe397fs (c.1188dup) is no gnomAD frequency available for this variant (gnomAD).

LAMA2 p.Phe397fs

c.1188dup · rs2482628074 · VCV2676256

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

congenital merosin-deficient muscular dystrophy 1A

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 8 of 65
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.8	GERP 1.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: LAMA2
Protein: p.Phe397fs
Coding: c.1188dup
MANE Select: NM_000426
dbSNP: rs2482628074
Type: Duplication
Location: chr6:129154664 (GRCh38)
Gene constraint: LOEUF 0.801 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 397: a UniProt-annotated variant site (in mdc1a); a UniProt-annotated variant site (in lgmdr23); the laminin egf-like 2 domain

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

Disease context

congenital merosin-deficient muscular dystrophy 1A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LAMA2 c.2749+2dup Pathogenic/Likely pathogenic ★★ same condition
LAMA2 p.Ala1696fs Pathogenic/Likely pathogenic ★★ same condition
LAMA2 p.Arg148fs Pathogenic ★★ same condition
LAMA2 p.Arg1566fs Pathogenic ★★ same condition
LAMA2 p.Asp2498fs Pathogenic ★★ same condition
LAMA2 p.Cys1420fs Likely pathogenic ★★ same condition
LAMA2 p.His3035fs Pathogenic ★★ same condition
LAMA2 p.Ile3033fs 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-phe397fs (accessed [today's date]).

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