Is OMP p.Arg39His (c.116G>A) pathogenic?

OMP p.Arg39His (c.116G>A) is classified Uncertain significance in OMP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-30). AlphaMissense: likely benign (0.2487); Ultra-rare (popmax 0.0706%, afr).

How common is OMP p.Arg39His (c.116G>A) in the general population?

OMP p.Arg39His (c.116G>A) is ultra-rare (popmax 0.0706%, afr) (gnomAD).

What do computational predictors say about OMP p.Arg39His (c.116G>A)?

AlphaMissense predicts likely benign (score 0.2487) — an in-silico prediction, not a clinical call.

OMP p.Arg39His

c.116G>A · VCV3302310

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2487 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0706%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

⚠ 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	0.2487	likely benign
REVEL	0.155	moderately benign-leaning
SaProt	LLR -7.32	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5.7	GERP 0.62, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 488 bp · p 0.42 · regional, not allelic
Overall
CADD	22.7	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 0.0706% African / African-American · 53/75,070 alleles

Filtering AF 0.0554% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.05%

Overall 0.00527% 85/1,613,248 alleles · ultra-rare exomes 53/1,460,874 · genomes 32/152,374 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0706%	1,416
Middle Eastern	0.0165%	6,060
Remaining individualsnot grpmax-eligible	0.016%	6,248
South Asian	0.00659%	15,181
Admixed American	0.00333%	30,018
East Asian	0.00223%	44,884
European (non-Finnish)	0.00102%	98,326

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.Arg39His
Coding: c.116G>A
MANE Select: NM_006189
Type: single nucleotide variant
Location: chr11:77102955 (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-arg39his (accessed [today's date]).

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