LRMDA p.Asn112=
c.336C>T · rs199857233 · VCV261989
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.512%, mid)
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 -6.7 | GERP -5.9 |
| Overall | ||
| CADD | 1.983 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.512%
Middle Eastern · 31/6,060 alleles
Filtering AF
0.37%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.332%
Overall
0.0581%
937/1,614,006 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.512% | 195 |
| South Asian | 0.378% | 265 |
| Remaining individualsnot grpmax-eligible | 0.0688% | 1,454 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0507% | 1,974 |
| European (non-Finnish) | 0.0396% | 2,527 |
| Finnishnot grpmax-eligible | 0.0375% | 2,668 |
| Admixed American | 0.0117% | 8,572 |
| East Asian | 0.00892% | 11,216 |
| African / African-American | 0.00267% | 37,506 |
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.Asn112=
- Coding
- c.336C>T
- MANE Select
- NM_001305581
- dbSNP
- rs199857233
- Type
- single nucleotide variant
- Location
- chr10:76047241 (GRCh38)
- Gene constraint
- LOEUF 0.958 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.40
- Residue 112
- the lrrct domain
Similar variants
- LRMDA p.Asn112Tyr Uncertain significance ★ ⚠ same residue
- 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
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-asn112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown