LAMA2 p.Pro189=
c.567G>A · rs746692025 · VCV1140724
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00769%, sas)
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 -4.7 | GERP -4.1 |
| Overall | ||
| CADD | 2.914 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00769%
South Asian · 7/91,072 alleles
Filtering AF
0.00359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00255%
Overall
0.000868%
14/1,613,786 alleles · very rare
exomes 11/1,461,772 · genomes 3/152,014 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00769% | 13,010 |
| Finnishnot grpmax-eligible | 0.00313% | 31,996 |
| African / African-American | 0.00267% | 37,430 |
| East Asian | 0.00223% | 44,890 |
| European (non-Finnish) | 0.00017% | 589,971 |
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.Pro189=
- Coding
- c.567G>A
- MANE Select
- NM_000426
- dbSNP
- rs746692025
- Type
- single nucleotide variant
- Location
- chr6:129098343 (GRCh38)
- Gene constraint
- LOEUF 0.801 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 189
- a UniProt-annotated variant site (in mdc1a); a UniProt-annotated variant site (in lgmdr23); the laminin n-terminal domain
Similar variants
- LAMA2 p.Pro189Leu 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
- LAMA2 c.1884+1G>A Pathogenic/Likely pathogenic ★★ same condition
- LAMA2 c.1884+2T>C 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-pro189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown