LRMDA p.Lys213=
c.639A>G · rs747816453 · VCV1681439
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
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 2 | GERP -4.8, phastCons 1 |
| Overall | ||
| CADD | 4.794 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,896 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.000496%
8/1,614,042 alleles · ultra-rare
exomes 6/1,461,870 · genomes 2/152,172 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,483 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,490 |
| European (non-Finnish) | 8.47e-05% | 1,180,020 |
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
- LRMDA
- Protein
- p.Lys213=
- Coding
- c.639A>G
- MANE Select
- NM_001305581
- dbSNP
- rs747816453
- Type
- single nucleotide variant
- Location
- chr10:76557246 (GRCh38)
- Gene constraint
- LOEUF 0.958 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.40
Similar variants
- LRMDA p.Arg184Cys Uncertain significance ★★ ⚠ same type
- LRMDA p.Arg207His Uncertain significance ★★ ⚠ same type
- LRMDA p.Met166Thr Uncertain significance ★★ ⚠ same type
- LRMDA p.Tyr129Cys Uncertain significance ★★ ⚠ same type
- LRMDA c.132-253009C>T Benign/Likely benign ★★ same type
- LRMDA c.398+31A>C Benign ★★ same type
- LRMDA c.516+53C>T Benign ★★ same type
- LRMDA c.601+18T>G 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/lrmda-p-lys213 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown