Is LTB4R2 p.Pro331Leu (c.992C>T) pathogenic?

LTB4R2 p.Pro331Leu (c.992C>T) is classified Uncertain significance in LTB4R2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-08). AlphaMissense: likely benign (0.086); Very rare (popmax 0.005%, amr).

How common is LTB4R2 p.Pro331Leu (c.992C>T) in the general population?

LTB4R2 p.Pro331Leu (c.992C>T) is very rare (popmax 0.005%, amr) (gnomAD).

What do computational predictors say about LTB4R2 p.Pro331Leu (c.992C>T)?

AlphaMissense predicts likely benign (score 0.086) — an in-silico prediction, not a clinical call.

LTB4R2 p.Pro331Leu

c.992C>T · rs756869639 · VCV3121396

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.086 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.086	likely benign
REVEL	0.058	moderately benign-leaning
SaProt	LLR -5.72	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 3.4	GERP 0.41, phastCons 0.2
Regional constraint	o/e 1.07	unconstrained · MANE · 1,073 bp · p 0.092 · regional, not allelic
Overall
CADD	19.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% Admixed American · 3/59,968 alleles

Filtering AF 0.0018% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00157%

Overall 0.00291% 47/1,612,878 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.0142%	7,057
Admixed Americangrpmax	0.005%	19,989
African / African-American	0.004%	24,977
European (non-Finnish)	0.00254%	39,317
Remaining individualsnot grpmax-eligible	0.0016%	62,440
South Asian	0.0011%	91,076

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Pro331Leu
Coding: c.992C>T
MANE Select: NM_001143919 · reported on NM_019839
dbSNP: rs756869639
Type: single nucleotide variant
Location: chr14:24311656 (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-pro331leu (accessed [today's date]).

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