LIG3 p.Ser444=
c.1332G>A · rs111958156 · VCV929075
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0389%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.41 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -3.4 |
| Overall | ||
| CADD | 0.337 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0389%
European (non-Finnish) · 459/1,179,522 alleles
Filtering AF
0.036%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0348%
Overall
0.0301%
485/1,613,086 alleles · ultra-rare
exomes 455/1,460,838 · genomes 30/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0389% | 2,570 |
| African / African-American | 0.02% | 4,999 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,246 |
| East Asian | 0.00223% | 44,854 |
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.Ser444=
- Coding
- c.1332G>A
- MANE Select
- NM_013975
- dbSNP
- rs111958156
- Type
- single nucleotide variant
- Location
- chr17:34992569 (GRCh38)
- Gene constraint
- LOEUF 0.627 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.11 · 13 PDB
- Residue 444
- a UniProt-annotated variant site (in mtdps20)
Similar variants
- LIG3 p.Ser444Leu Uncertain significance ★ ⚠ same residue
- 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
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-ser444 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown