LIG4 p.Val403=
c.1209G>T · rs778437045 · VCV2724100
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,612,770)
Conditions
1
DNA ligase IV deficiency
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 -0.26 | GERP -5.3, phastCons 0.23 |
| Overall | ||
| CADD | 2.828 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,612,770). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- LIG4
- Protein
- p.Val403=
- Coding
- c.1209G>T
- MANE Select
- NM_206937
- dbSNP
- rs778437045
- Type
- single nucleotide variant
- Location
- chr13:108210060 (GRCh38)
- Gene constraint
- LOEUF 1.043 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.44 · 32 PDB
Disease context
DNA ligase IV deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor LIG4 syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- LIG4 p.Val403Ala Uncertain significance ★ ⚠ same residue
- LIG4 p.Arg278His Pathogenic ★★ same condition
- LIG4 p.Arg278Leu Pathogenic ★★ same condition
- LIG4 p.Arg293Ter Pathogenic/Likely pathogenic ★★ same condition
- LIG4 p.Arg580Ter Pathogenic/Likely pathogenic ★★ same condition
- LIG4 p.Arg814Ter Pathogenic/Likely pathogenic ★★ same condition
- LIG4 p.Gln74Ter Pathogenic/Likely pathogenic ★★ same condition
- LIG4 p.Gln773Ter Pathogenic/Likely pathogenic ★★ same condition
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/lig4-p-val403 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown