Is OGA p.Asp367Val (c.1100A>T) pathogenic?

OGA p.Asp367Val (c.1100A>T) is classified Uncertain significance in OGA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-11). AlphaMissense: ambiguous (0.4958); Very rare (popmax 0.000763%, nfe).

How common is OGA p.Asp367Val (c.1100A>T) in the general population?

OGA p.Asp367Val (c.1100A>T) is very rare (popmax 0.000763%, nfe) (gnomAD).

What do computational predictors say about OGA p.Asp367Val (c.1100A>T)?

AlphaMissense predicts ambiguous (score 0.4958) — an in-silico prediction, not a clinical call.

OGA p.Asp367Val

c.1100A>T · VCV4560794

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4958 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000763%, nfe)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Computational evidence

Protein change
AlphaMissense	0.4958	ambiguous
REVEL	0.103	moderately benign-leaning
SaProt	LLR -5.48	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>C here scores Δ0.93 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.9	GERP 2.8, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 2,325 bp · p 0.00049 · regional, not allelic
Overall
CADD	24.4	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 0.000763% European (non-Finnish) · 9/1,178,816 alleles

Filtering AF 0.000359% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00026%

Overall 0.000558% 9/1,612,766 alleles · very rare exomes 7/1,460,538 · genomes 2/152,228 · 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.Asp367Val
Coding: c.1100A>T
MANE Select: NM_012215
Type: single nucleotide variant
Location: chr10:101800337 (GRCh38)
Gene constraint: LOEUF 0.32 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.02 · 29 PDB

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

Similar variants

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
OGA p.Ala51Val 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-asp367val (accessed [today's date]).

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