LEMD3 p.Ala2=
c.6G>A · rs1868436630 · VCV2784731
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00114%, sas)
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 2.1, phastCons 1 |
| Overall | ||
| CADD | 15.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00114%
South Asian · 1/87,582 alleles
Overall
0.000126%
2/1,587,854 alleles · very rare
exomes 2/1,435,550 · genomes 0/152,304 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00114% | 87,582 |
| European (non-Finnish) | 8.55e-05% | 1,169,251 |
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
- LEMD3
- Protein
- p.Ala2=
- Coding
- c.6G>A
- MANE Select
- NM_014319
- dbSNP
- rs1868436630
- Type
- single nucleotide variant
- Location
- chr12:65169602 (GRCh38)
- Gene constraint
- LOEUF 0.584 · pLI 0.40 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.07 · 3 PDB
- Residue 2
- a modified residue (n-acetylalanine)
Similar variants
- LEMD3 p.Ala2Glu Uncertain significance ★ ⚠ same residue
- LEMD3 p.Arg537Ter Pathogenic ★★ same type
- LEMD3 p.Arg625Ter Pathogenic ★★ same type
- LEMD3 p.Arg655Ter Pathogenic/Likely pathogenic ★★ same type
- LEMD3 p.Arg678Ter Pathogenic/Likely pathogenic ★★ same type
- LEMD3 p.Arg735Ter Pathogenic ★★ same type
- LEMD3 p.Glu601Ter Pathogenic/Likely pathogenic ★★ same type
- LEMD3 p.Tyr441Ter Pathogenic ★★ same type
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/lemd3-p-ala2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown