Is OGA p.Ser19Ala (c.55T>G) pathogenic?

OGA p.Ser19Ala (c.55T>G) is classified Uncertain significance in OGA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-22). AlphaMissense: likely benign (0.0541); Very rare (popmax 0.00111%, nfe).

How common is OGA p.Ser19Ala (c.55T>G) in the general population?

OGA p.Ser19Ala (c.55T>G) is very rare (popmax 0.00111%, nfe) (gnomAD).

What do computational predictors say about OGA p.Ser19Ala (c.55T>G)?

AlphaMissense predicts likely benign (score 0.0541) — an in-silico prediction, not a clinical call.

OGA p.Ser19Ala

c.55T>G · VCV4560795

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0541 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00111%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0541	likely benign
REVEL	0.063	moderately benign-leaning
SaProt	LLR -6.39	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.2	GERP -1.8, phastCons 0.92
Regional constraint	o/e 1.36	unconstrained · MANE · 183 bp · p 0.00073 · regional, not allelic
Overall
CADD	14.61	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00111% European (non-Finnish) · 13/1,175,206 alleles

Filtering AF 0.000617% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000476%

Overall 0.00081% 13/1,604,836 alleles · very rare exomes 13/1,452,628 · genomes 0/152,208 · 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: OGA
Protein: p.Ser19Ala
Coding: c.55T>G
MANE Select: NM_012215
Type: single nucleotide variant
Location: chr10:101817968 (GRCh38)
Gene constraint: LOEUF 0.32 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.02 · 29 PDB
Residue 19: the 'disordered' region

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

Similar variants

OGA p.Ser19Cys Uncertain significance ★ ⚠ same residue
OGA c.1037-3C>T Likely benign ★★ same type
OGA p.Ala25Pro Uncertain significance ★ ⚠ same type
OGA p.Ala25Val Uncertain significance ★ ⚠ same type
OGA p.Ala27Val Uncertain significance ★ ⚠ same type
OGA p.Ala33Val Uncertain significance ★ ⚠ same type
OGA p.Ala45Val Uncertain significance ★ ⚠ same type
OGA p.Ala490Val Uncertain significance ★ ⚠ 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/oga-p-ser19ala (accessed [today's date]).

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