Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.613%, 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 0.26 | GERP -2, phastCons 0.94 |
| Overall | ||
| CADD | 9.817 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.613%
East Asian · 275/44,852 alleles
Filtering AF
0.554%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.53%
Overall
0.0215%
347/1,613,854 alleles · rare
exomes 302/1,461,564 · genomes 45/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.613% | 163 |
| Remaining individualsnot grpmax-eligible | 0.0928% | 1,077 |
| Admixed American | 0.00667% | 14,985 |
| South Asian | 0.0011% | 91,050 |
| European (non-Finnish) | 0.000763% | 131,100 |
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
- LIG3
- Protein
- p.Val461=
- Coding
- c.1383G>A
- MANE Select
- NM_013975
- dbSNP
- rs3135988
- Type
- single nucleotide variant
- Location
- chr17:34992620 (GRCh38)
- Gene constraint
- LOEUF 0.627 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.11 · 13 PDB
- Residue 461
- a UniProt-annotated variant site (in mtdps20)
Similar variants
- LIG3 c.1209-2A>G Pathogenic/Likely pathogenic ★★ same type
- LIG3 p.Arg648Gln Uncertain significance ★★ ⚠ same type
- LIG3 p.Gln398Arg Uncertain significance ★★ ⚠ same type
- LIG3 p.Ser248Asn Uncertain significance ★★ ⚠ same type
- LIG3 c.1041+11C>T Benign ★★ same type
- LIG3 c.1912-3C>T Benign/Likely benign ★★ same type
- LIG3 c.2331+19G>A Benign ★★ same type
- LIG3 c.2796+6G>A 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/lig3-p-val461 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown