Is LIG1 p.Asp50= (c.150C>T) pathogenic?

LIG1 p.Asp50= (c.150C>T) is classified Likely benign in LIG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-24). Very rare (popmax 0.000254%, nfe).

How common is LIG1 p.Asp50= (c.150C>T) in the general population?

LIG1 p.Asp50= (c.150C>T) is very rare (popmax 0.000254%, nfe) (gnomAD).

LIG1 p.Asp50=

c.150C>T · VCV4803147

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000254%, nfe)

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 0.5	GERP 0.66, phastCons 0.99
Overall
CADD	6.243	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000254% European (non-Finnish) · 3/1,180,030 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000186% 3/1,614,166 alleles · very rare exomes 3/1,461,876 · genomes 0/152,290 · joint denominator

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: LIG1
Protein: p.Asp50=
Coding: c.150C>T
MANE Select: NM_000234
Type: single nucleotide variant
Location: chr19:48161465 (GRCh38)
Structure: AlphaFold pLDDT 75.13 · 2 PDB
Residue 50: the lrrnt domain

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

Similar variants

LIG1 p.Asp50Tyr Uncertain significance ★ ⚠ same residue
LIG1 p.Ala269Thr Uncertain significance ★★ ⚠ same type
LIG1 p.Ala293Val 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-asp50 (accessed [today's date]).

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