Is OMP p.Pro151Arg (c.452C>G) pathogenic?

OMP p.Pro151Arg (c.452C>G) is classified Uncertain significance in OMP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-12). AlphaMissense: ambiguous (0.4038); Very rare (popmax 0.000509%, nfe).

How common is OMP p.Pro151Arg (c.452C>G) in the general population?

OMP p.Pro151Arg (c.452C>G) is very rare (popmax 0.000509%, nfe) (gnomAD).

What do computational predictors say about OMP p.Pro151Arg (c.452C>G)?

AlphaMissense predicts ambiguous (score 0.4038) — an in-silico prediction, not a clinical call.

OMP p.Pro151Arg

c.452C>G · VCV3924139

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4038 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000509%, nfe)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.4038	ambiguous
REVEL	0.35	indeterminate
SaProt	LLR -10.80	damaging
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5.8	GERP 1.8, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 488 bp · p 0.42 · regional, not allelic
Overall
CADD	23.4	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 0.000509% European (non-Finnish) · 6/1,179,516 alleles

Filtering AF 0.000183% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00012%

Overall 0.000372% 6/1,612,536 alleles · very rare exomes 6/1,460,298 · genomes 0/152,238 · 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: OMP
Protein: p.Pro151Arg
Coding: c.452C>G
MANE Select: NM_006189
Type: single nucleotide variant
Location: chr11:77103291 (GRCh38)

Full OMP 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/omp-p-pro151arg (accessed [today's date]).

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