ASMT p.Lys81Glu
c.241A>G · rs117343570 · VCV599440
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.21%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.107 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -7 | GERP -2.6 |
| Regional constraint | o/e 1.20 | unconstrained · MANE · 28 kb · p 2e-05 · regional, not allelic |
| Overall | ||
| CADD | 0.004 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.21%
African / African-American · 905/75,018 alleles
Filtering AF
1.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.12%
Overall
0.0636%
1,026/1,613,896 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.21% | 83 |
| Middle Eastern | 0.0993% | 1,007 |
| Admixed American | 0.08% | 1,250 |
| Remaining individualsnot grpmax-eligible | 0.0704% | 1,420 |
| South Asian | 0.00329% | 30,358 |
| European (non-Finnish) | 0.0017% | 58,993 |
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
- ASMT
- Protein
- p.Lys81Glu
- Coding
- c.241A>G
- MANE Select
- NM_001171038
- dbSNP
- rs117343570
- Type
- single nucleotide variant
- Location
- chrX:1623310 (GRCh38)
- Structure
- AlphaFold pLDDT 95.55 · 2 PDB
- Residue 81
- a UniProt-annotated variant site (no effect on enzyme activity); a β-strand
Similar variants
- ASMT c.562+2T>C Conflicting classifications of pathogenicity ★ same type
- ASMT p.Asn17Lys Uncertain significance ★ same type
- ASMT p.Cys29Ter Uncertain significance ★ same type
- ASMT p.Phe266Val Uncertain significance ★ same type
- ASMT p.Tyr229Ter Uncertain significance ★ same type
- ASMT p.Val236Ile Uncertain significance ★ same type
- ASMT p.Arg210= Likely benign same type
- ASMT p.Asp122= 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/asmt-p-lys81glu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown