LMOD2 p.Tyr13=
c.39C>T · VCV4897640
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.432%, afr)
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 -0.027 | GERP -0.4, phastCons 0.92 |
| Overall | ||
| CADD | 8.441 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.432%
African / African-American · 324/74,956 alleles
Filtering AF
0.394%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.378%
Overall
0.0262%
422/1,608,782 alleles · rare
exomes 235/1,456,538 · genomes 187/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.432% | 231 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0441% | 2,265 |
| Admixed American | 0.0439% | 2,280 |
| Remaining individualsnot grpmax-eligible | 0.0353% | 2,833 |
| South Asian | 0.0201% | 4,987 |
| Middle Eastern | 0.0165% | 6,058 |
| European (non-Finnish) | 0.00153% | 65,436 |
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.Tyr13=
- Coding
- c.39C>T
- MANE Select
- NM_207163
- Type
- single nucleotide variant
- Location
- chr7:123656002 (GRCh38)
- Gene constraint
- LOEUF 0.984 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.14 · 6 PDB
- Residue 13
- the 'interaction with actin 1' region; the 'interaction with tropomyosin alpha' region; a turn
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-tyr13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown