Is OMP p.Val143Ile (c.427G>A) pathogenic?

OMP p.Val143Ile (c.427G>A) is classified Likely benign in OMP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-18). AlphaMissense: likely benign (0.0524); Ultra-rare (popmax 0.0178%, eas).

How common is OMP p.Val143Ile (c.427G>A) in the general population?

OMP p.Val143Ile (c.427G>A) is ultra-rare (popmax 0.0178%, eas) (gnomAD).

What do computational predictors say about OMP p.Val143Ile (c.427G>A)?

AlphaMissense predicts likely benign (score 0.0524) — an in-silico prediction, not a clinical call.

OMP p.Val143Ile

c.427G>A · VCV3302309

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0524 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0178%, eas)

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	0.0524	likely benign
REVEL	0.018	moderately benign-leaning
SaProt	LLR -6.97	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.12	GERP -1.4
Regional constraint	o/e 1.05	unconstrained · MANE · 488 bp · p 0.42 · regional, not allelic
Overall
CADD	15.61	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 0.0178% East Asian · 8/44,884 alleles

Filtering AF 0.00883% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00641%

Overall 0.00285% 46/1,613,190 alleles · ultra-rare exomes 39/1,461,048 · genomes 7/152,142 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0178%	5,611
Middle Eastern	0.0164%	6,084
Admixed American	0.015%	6,667
South Asian	0.00439%	22,770
Remaining individualsnot grpmax-eligible	0.0032%	31,227
African / African-American	0.00267%	37,456
European (non-Finnish)	0.0017%	58,994

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.Val143Ile
Coding: c.427G>A
MANE Select: NM_006189
Type: single nucleotide variant
Location: chr11:77103266 (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-val143ile (accessed [today's date]).

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