LAMA2 p.Phe504=
c.1512C>T · rs2115033482 · VCV1648316
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 4.9 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 12.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- LAMA2
- Protein
- p.Phe504=
- Coding
- c.1512C>T
- MANE Select
- NM_000426
- dbSNP
- rs2115033482
- Type
- single nucleotide variant
- Location
- chr6:129190249 (GRCh38)
- Gene constraint
- LOEUF 0.801 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 504
- a UniProt-annotated variant site (in mdc1a); a UniProt-annotated variant site (in lgmdr23); the laminin egf-like 4 domain
Similar variants
- 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
- LAMA2 c.1885-1G>A 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-phe504 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown