Is OMG p.Val172= (c.516G>A) pathogenic?

OMG p.Val172= (c.516G>A) is classified Likely benign in OMG (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-12-28). Very rare (popmax 8.47e-05%, nfe); Associated with OMG-related disorder.

What condition is associated with OMG p.Val172= (c.516G>A)?

OMG p.Val172= (c.516G>A) is associated with OMG-related disorder (ClinVar).

How common is OMG p.Val172= (c.516G>A) in the general population?

OMG p.Val172= (c.516G>A) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

OMG p.Val172=

c.516G>A · rs777337623 · VCV3029883

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

OMG-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.8	GERP 1, phastCons 1
Overall
CADD	7.677	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,012 alleles

Overall 6.2e-05% 1/1,614,084 alleles · very rare exomes 1/1,461,854 · genomes 0/152,230 · 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: OMG
Protein: p.Val172=
Coding: c.516G>A
MANE Select: NM_002544
dbSNP: rs777337623
Type: single nucleotide variant
Location: chr17:31295816 (GRCh38)
Gene constraint: LOEUF 0.565 · pLI 0.90 (gnomAD)
Structure: AlphaFold pLDDT 67.94

Full OMG gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

OMG-related disorder

Similar variants

OMG p.Pro333Ser Uncertain significance ★ ⚠ same type
OMG p.Val411= Likely benign ★ same type

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/omg-p-val172 (accessed [today's date]).

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