LAMA2 p.Pro81=
c.243G>A · rs766642494 · VCV1596629
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
1
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 -4.9 | GERP -3.8 |
| Overall | ||
| CADD | 5.673 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,024 alleles
Filtering AF
0.000292%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000211%
Overall
0.00062%
10/1,614,122 alleles · very rare
exomes 10/1,461,854 · genomes 0/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 75,024 |
| South Asian | 0.0011% | 91,080 |
| European (non-Finnish) | 0.000678% | 147,501 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- LAMA2
- Protein
- p.Pro81=
- Coding
- c.243G>A
- MANE Select
- NM_000426
- dbSNP
- rs766642494
- Type
- single nucleotide variant
- Location
- chr6:129050048 (GRCh38)
- Gene constraint
- LOEUF 0.801 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 81
- the laminin n-terminal domain
Similar variants
- LAMA2 p.Pro81Leu Uncertain significance ★ ⚠ same residue
- LAMA2 p.Pro81fs Pathogenic ★ same residue
- LAMA2 p.Pro81Ala Uncertain significance ★ same residue
- 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
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-pro81 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown