Is LIG1 p.Ser191= (c.573C>T) pathogenic?

LIG1 p.Ser191= (c.573C>T) is classified Uncertain significance in LIG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-02). Very rare (popmax 8.52e-05%, nfe).

How common is LIG1 p.Ser191= (c.573C>T) in the general population?

LIG1 p.Ser191= (c.573C>T) is very rare (popmax 8.52e-05%, nfe) (gnomAD).

LIG1 p.Ser191=

c.573C>T · rs2514250274 · VCV2070000

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.52e-05%, 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 0.64	GERP -2.8, phastCons 0.002
Overall
CADD	2.186	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.52e-05% European (non-Finnish) · 1/1,173,632 alleles

Overall 6.22e-05% 1/1,607,032 alleles · very rare exomes 1/1,454,844 · genomes 0/152,188 · 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.Ser191=
Coding: c.573C>T
MANE Select: NM_000234
dbSNP: rs2514250274
Type: single nucleotide variant
Location: chr19:48151233 (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.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
LIG1 p.Ala708Thr 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-ser191 (accessed [today's date]).

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