LIG3 p.Ser476=
c.1428G>A · VCV3375328
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0333%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.5 | GERP -3.7 |
| Overall | ||
| CADD | 0.669 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0333%
Middle Eastern · 2/6,000 alleles
Filtering AF
0.00587%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00244%
Overall
0.00162%
26/1,608,092 alleles · ultra-rare
exomes 23/1,455,940 · genomes 3/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0333% | 3,000 |
| African / African-American | 0.00268% | 37,356 |
| European (non-Finnish) | 0.00187% | 53,519 |
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.Ser476=
- Coding
- c.1428G>A
- MANE Select
- NM_013975
- Type
- single nucleotide variant
- Location
- chr17:34992665 (GRCh38)
- Gene constraint
- LOEUF 0.627 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.11 · 13 PDB
- Residue 476
- 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-ser476 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown