Is LTB4R2 p.Arg52Pro (c.155G>C) pathogenic?

LTB4R2 p.Arg52Pro (c.155G>C) is classified Uncertain significance in LTB4R2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-28). AlphaMissense: likely benign (0.074); Very rare (popmax 0.00134%, afr).

How common is LTB4R2 p.Arg52Pro (c.155G>C) in the general population?

LTB4R2 p.Arg52Pro (c.155G>C) is very rare (popmax 0.00134%, afr) (gnomAD).

What do computational predictors say about LTB4R2 p.Arg52Pro (c.155G>C)?

AlphaMissense predicts likely benign (score 0.074) — an in-silico prediction, not a clinical call.

LTB4R2 p.Arg52Pro

c.155G>C · VCV3292197

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.074 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.074	likely benign
REVEL	0.084	moderately benign-leaning
SaProt	LLR -11.01	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.9	GERP -2.8, phastCons 0.043
Regional constraint	o/e 1.07	unconstrained · MANE · 1,073 bp · p 0.092 · regional, not allelic
Overall
CADD	18.68	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,784 alleles

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

Overall 0.000277% 4/1,442,760 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00134%	74,784
European (non-Finnish)	0.000256%	391,192

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.Arg52Pro
Coding: c.155G>C
MANE Select: NM_001393339 · reported on NM_019839
Type: single nucleotide variant
Location: chr14:24310819 (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-arg52pro (accessed [today's date]).

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