LAMA2 p.Ser2452=
c.7356G>A · rs758085712 · VCV1153211
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00447%, eas)
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 0.045 | GERP -4.3, phastCons 0.015 |
| Overall | ||
| CADD | 3.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00447%
East Asian · 2/44,732 alleles
Filtering AF
0.000741%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00054%
Overall
0.0013%
21/1,609,880 alleles · very rare
exomes 20/1,458,008 · genomes 1/151,872 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00447% | 22,366 |
| Admixed American | 0.00334% | 29,941 |
| Finnishnot grpmax-eligible | 0.00313% | 31,941 |
| European (non-Finnish) | 0.00119% | 84,060 |
| South Asian | 0.0011% | 90,990 |
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.Ser2452=
- Coding
- c.7356G>A
- MANE Select
- NM_000426
- dbSNP
- rs758085712
- Type
- single nucleotide variant
- Location
- chr6:129473269 (GRCh38)
- Gene constraint
- LOEUF 0.801 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 2452
- a UniProt-annotated variant site (in mdc1a); a UniProt-annotated variant site (in lgmdr23); the laminin g-like 2 domain
Similar variants
- LAMA2 p.Ser2452Leu Uncertain significance ★★ ⚠ same residue
- LAMA2 p.Ser2452Thr 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
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-ser2452 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown