Is LTB4R2 p.Thr188= (c.564C>T) pathogenic?

LTB4R2 p.Thr188= (c.564C>T) is classified Benign in LTB4R2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-06-11). Common (popmax 7.7%, afr) — too common for a highly-penetrant pathogenic allele.

LTB4R2 p.Thr188=

Q: How common is LTB4R2 p.Thr188= (c.564C>T) in the general population?

LTB4R2 p.Thr188= (c.564C>T) is common (popmax 7.7%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.564C>T · rs1950503 · VCV768643

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 7.7%, afr) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -20	GERP -3.5
Overall
CADD	0.707	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 7.7% African / African-American · 5,756/74,742 alleles

Filtering AF 7.53% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.47%

Overall 0.396% 6,369/1,608,928 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	7.7%	13
Remaining individualsnot grpmax-eligible	0.461%	217
Admixed American	0.411%	244
Middle Eastern	0.198%	504
South Asian	0.0222%	4,511
European (non-Finnish)	0.00416%	24,043

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: LTB4R2
Protein: p.Thr188=
Coding: c.564C>T
MANE Select: NM_001393339 · reported on NM_019839
dbSNP: rs1950503
Type: single nucleotide variant
Location: chr14:24311228 (GRCh38)

Full LTB4R2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/ltb4r2-p-thr188 (accessed [today's date]).

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