Is OMG p.Ser417= (c.1251T>G) pathogenic?

OMG p.Ser417= (c.1251T>G) is classified Likely benign in OMG (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-03-27). Ultra-rare (popmax 0.0107%, afr); Associated with OMG-related disorder.

What condition is associated with OMG p.Ser417= (c.1251T>G)?

OMG p.Ser417= (c.1251T>G) is associated with OMG-related disorder (ClinVar).

How common is OMG p.Ser417= (c.1251T>G) in the general population?

OMG p.Ser417= (c.1251T>G) is ultra-rare (popmax 0.0107%, afr) (gnomAD).

OMG p.Ser417=

c.1251T>G · rs747451047 · VCV3054841

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, afr)

Conditions

OMG-related disorder

⚠ 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
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.4	GERP 0.33, phastCons 0.64
Overall
CADD	4.93	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0107% African / African-American · 8/74,952 alleles

Filtering AF 0.00528% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0038%

Overall 0.000929% 15/1,614,060 alleles · ultra-rare exomes 10/1,461,836 · genomes 5/152,224 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0107%	9,369
Remaining individualsnot grpmax-eligible	0.0016%	62,482
European (non-Finnish)	0.000508%	196,670

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.Ser417=
Coding: c.1251T>G
MANE Select: NM_002544
dbSNP: rs747451047
Type: single nucleotide variant
Location: chr17:31295081 (GRCh38)

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

Disease context

OMG-related disorder

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-ser417 (accessed [today's date]).

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