LMOD2 p.Pro430=
c.1290T>C · VCV4897660
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0645%, amr)
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 -8.7 | GERP -3 |
| Overall | ||
| CADD | 0.254 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0645%
Admixed American · 22/34,120 alleles
Filtering AF
0.0436%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0368%
Overall
0.0161%
160/991,878 alleles · ultra-rare
exomes 141/904,350 · genomes 19/87,528 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0645% | 1,551 |
| South Asian | 0.0444% | 2,255 |
| Middle Eastern | 0.0388% | 2,580 |
| Finnishnot grpmax-eligible | 0.0226% | 4,417 |
| East Asian | 0.016% | 6,255 |
| Remaining individualsnot grpmax-eligible | 0.0141% | 7,067 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0125% | 8,015 |
| European (non-Finnish) | 0.0122% | 8,168 |
| African / African-American | 0.00461% | 21,708 |
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.Pro430=
- Coding
- c.1290T>C
- MANE Select
- NM_207163
- Type
- single nucleotide variant
- Location
- chr7:123662876 (GRCh38)
- Gene constraint
- LOEUF 0.984 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.14 · 6 PDB
- Residue 430
- a UniProt-annotated variant site (in cmd2g; no protein detected by western blot in cardiac tissue from a homozygous patient); the 'interaction with actin 2' 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.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-pro430 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown