Is LIG1 p.Ala293= (c.879C>T) pathogenic?

LIG1 p.Ala293= (c.879C>T) is classified Likely benign in LIG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-03). Absent from gnomAD v4.1.

How common is LIG1 p.Ala293= (c.879C>T) in the general population?

LIG1 p.Ala293= (c.879C>T) is absent from gnomAD v4.1 (gnomAD).

LIG1 p.Ala293=

c.879C>T · VCV3722193

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 1.1	GERP -2.3, phastCons 1
Overall
CADD	8.231	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: LIG1
Protein: p.Ala293=
Coding: c.879C>T
MANE Select: NM_000234
Type: single nucleotide variant
Location: chr19:48143578 (GRCh38)
Structure: AlphaFold pLDDT 75.13 · 2 PDB

Full LIG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

LIG1 p.Ala293Val Uncertain significance ★★ ⚠ same residue
LIG1 p.Ala293Ser Uncertain significance ★ ⚠ same residue
LIG1 p.Ala269Thr 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
LIG1 p.Ala578Thr 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-ala293 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown