LIG1 p.Arg409=
c.1227C>G · rs142732689 · VCV1612028
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.036%, 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 -7.7 | GERP -2.7 |
| Overall | ||
| CADD | 0.197 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.036%
African / African-American · 27/75,058 alleles
Filtering AF
0.0254%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0218%
Overall
0.00298%
48/1,613,270 alleles · ultra-rare
exomes 42/1,460,930 · genomes 6/152,340 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.036% | 2,780 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,976 |
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
- LIG1
- Protein
- p.Arg409=
- Coding
- c.1227C>G
- MANE Select
- NM_000234
- dbSNP
- rs142732689
- Type
- single nucleotide variant
- Location
- chr19:48137549 (GRCh38)
- Structure
- AlphaFold pLDDT 75.13 · 2 PDB
Similar variants
- LIG1 p.Arg409His Benign ★★ same residue
- LIG1 p.Arg409Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
- LIG1 p.Ala269Thr Uncertain significance ★★ ⚠ same type
- LIG1 p.Ala293Val Uncertain significance ★★ ⚠ same type
- LIG1 p.Ala412Thr Uncertain significance ★★ ⚠ same type
- LIG1 p.Ala443Thr Uncertain significance ★★ ⚠ same type
- LIG1 p.Ala462Ser Uncertain significance ★★ ⚠ same type
- LIG1 p.Ala545Gly Uncertain significance ★★ ⚠ 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/lig1-p-arg409 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown