LMOD2 p.Asp201=
c.603C>T · VCV4897650
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
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 -5.7 | GERP -4.3 |
| Overall | ||
| CADD | 2.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,880 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.000558%
9/1,613,822 alleles · very rare
exomes 8/1,461,618 · genomes 1/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,960 |
| Admixed American | 0.00667% | 14,999 |
| African / African-American | 0.00133% | 74,932 |
| European (non-Finnish) | 8.48e-05% | 1,179,898 |
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.Asp201=
- Coding
- c.603C>T
- MANE Select
- NM_207163
- Type
- single nucleotide variant
- Location
- chr7:123662189 (GRCh38)
- Gene constraint
- LOEUF 0.984 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.14 · 6 PDB
- Residue 201
- an α-helix; the 'interaction with actin 2' 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.Glu100= Benign ★★ same type
- LMOD2 p.Ile221Thr Likely benign ★★ ⚠ 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-asp201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown