LAMA2 p.Phe1975=
c.5925C>T · rs1243474580 · VCV1133475
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
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 | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -4.2 |
| Overall | ||
| CADD | 3.779 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,856 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,613,860 alleles · very rare
exomes 2/1,461,542 · genomes 0/152,318 · joint denominator
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.Phe1975=
- Coding
- c.5925C>T
- MANE Select
- NM_000426
- dbSNP
- rs1243474580
- Type
- single nucleotide variant
- Location
- chr6:129427811 (GRCh38)
- Gene constraint
- LOEUF 0.801 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 1975
- a UniProt-annotated variant site (in mdc1a); a UniProt-annotated variant site (in lgmdr23); the 'domain ii and i' region
Similar variants
- LAMA2 p.Phe1975Val Likely benign ★ 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-phe1975 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown