LMOD2 p.Glu100=
c.300A>G · rs7809453 · VCV1263755
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 65.6%, sas) — too common for a highly-penetrant pathogenic allele
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 | GERP -3.4, phastCons 1 |
| Overall | ||
| CADD | 5.609 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
65.6%
South Asian · 52,981/80,784 alleles
Filtering AF
65.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 64.9%
Overall
47.3%
725,632/1,533,068 alleles · common
exomes 655,960/1,381,046 · genomes 69,672/152,022 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 65.6% | 2 |
| Amishnot grpmax-eligible | 60.2% | 2 |
| East Asian | 56.2% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 51.5% | 2 |
| Middle Eastern | 51.4% | 2 |
| Remaining individualsnot grpmax-eligible | 48.5% | 2 |
| Finnishnot grpmax-eligible | 46.9% | 2 |
| Admixed American | 46.2% | 2 |
| European (non-Finnish) | 46% | 2 |
| African / African-American | 40.4% | 2 |
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
- LMOD2
- Protein
- p.Glu100=
- Coding
- c.300A>G
- MANE Select
- NM_207163
- dbSNP
- rs7809453
- Type
- single nucleotide variant
- Location
- chr7:123661886 (GRCh38)
- Gene constraint
- LOEUF 0.984 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.14 · 6 PDB
- Residue 100
- the 'interaction with actin 1' region; the 'disordered' region
Similar variants
- LMOD2 p.Arg231Cys Uncertain significance ★★ ⚠ same type
- LMOD2 p.Glu276Lys Uncertain significance ★★ ⚠ same type
- LMOD2 p.Thr244Met Uncertain significance ★★ ⚠ same type
- LMOD2 c.1617+220A>G Benign ★★ same type
- LMOD2 c.273+30C>A Benign ★★ same type
- LMOD2 c.-54C>T Benign ★★ same type
- LMOD2 p.Ile221Thr Likely benign ★★ ⚠ same type
- LMOD2 p.Arg513Ter 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/lmod2-p-glu100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown