Is OMP p.Arg67Cys (c.199C>T) pathogenic?

OMP p.Arg67Cys (c.199C>T) is classified Uncertain significance in OMP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-28). AlphaMissense: likely benign (0.1325); Very rare (popmax 0.00446%, eas).

How common is OMP p.Arg67Cys (c.199C>T) in the general population?

OMP p.Arg67Cys (c.199C>T) is very rare (popmax 0.00446%, eas) (gnomAD).

What do computational predictors say about OMP p.Arg67Cys (c.199C>T)?

AlphaMissense predicts likely benign (score 0.1325) — an in-silico prediction, not a clinical call.

OMP p.Arg67Cys

c.199C>T · rs782366056 · VCV3204308

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1325 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00446%, eas)

Missense predictors

1/3 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	0.1325	likely benign
REVEL	0.143	moderately benign-leaning
SaProt	LLR -10.20	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 5.8	GERP 0.68, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 488 bp · p 0.42 · regional, not allelic
Overall
CADD	24.2	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 0.00446% East Asian · 2/44,892 alleles

Filtering AF 0.000953% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000787%

Overall 0.00155% 25/1,613,448 alleles · very rare exomes 23/1,461,240 · genomes 2/152,208 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00446%	22,446
South Asian	0.00329%	30,359
Admixed American	0.00167%	60,004
European (non-Finnish)	0.00153%	65,550
African / African-American	0.00133%	74,936

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.Arg67Cys
Coding: c.199C>T
MANE Select: NM_006189
dbSNP: rs782366056
Type: single nucleotide variant
Location: chr11:77103038 (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-arg67cys (accessed [today's date]).

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