Is OMP p.Asn86Lys (c.258C>G) pathogenic?

OMP p.Asn86Lys (c.258C>G) is classified Uncertain significance in OMP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-17). AlphaMissense: likely pathogenic (0.6265); Ultra-rare (popmax 0.0164%, mid).

How common is OMP p.Asn86Lys (c.258C>G) in the general population?

OMP p.Asn86Lys (c.258C>G) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

What do computational predictors say about OMP p.Asn86Lys (c.258C>G)?

AlphaMissense predicts likely pathogenic (score 0.6265) — an in-silico prediction, not a clinical call.

OMP p.Asn86Lys

c.258C>G · rs532565906 · VCV3204311

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6265 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Missense predictors

2/3 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	0.6265	likely pathogenic
REVEL	0.078	moderately benign-leaning
SaProt	LLR -10.01	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.4	GERP -0.49, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 488 bp · p 0.42 · regional, not allelic
Overall
CADD	22.4	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 0.0164% Middle Eastern · 1/6,084 alleles

Filtering AF 0.00359% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00255%

Overall 0.00279% 45/1,613,800 alleles · ultra-rare exomes 43/1,461,550 · genomes 2/152,250 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,084
South Asian	0.00769%	13,012
Remaining individualsnot grpmax-eligible	0.0048%	20,821
European (non-Finnish)	0.00288%	34,703

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.Asn86Lys
Coding: c.258C>G
MANE Select: NM_006189
dbSNP: rs532565906
Type: single nucleotide variant
Location: chr11:77103097 (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-asn86lys (accessed [today's date]).

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