Is OGT p.Arg70Ser (c.210G>T) pathogenic?

OGT p.Arg70Ser (c.210G>T) is classified Uncertain significance in OGT (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-18). AlphaMissense: likely pathogenic (0.9503); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with OGT p.Arg70Ser (c.210G>T)?

OGT p.Arg70Ser (c.210G>T) is associated with Inborn genetic diseases (ClinVar).

How common is OGT p.Arg70Ser (c.210G>T) in the general population?

OGT p.Arg70Ser (c.210G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about OGT p.Arg70Ser (c.210G>T)?

AlphaMissense predicts likely pathogenic (score 0.9503) — an in-silico prediction, not a clinical call.

OGT p.Arg70Ser

c.210G>T · rs2522816079 · VCV2538306

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9503 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9503	likely pathogenic
REVEL	0.343	indeterminate
SaProt	LLR -8.93	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.5	GERP 1.6, phastCons 1
Regional constraint	o/e 0.32	constrained · MANE · 4,749 bp · p 2.7e-13 · regional, not allelic
Overall
CADD	26.3	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: OGT
Protein: p.Arg70Ser
Coding: c.210G>T
MANE Select: NM_181672
dbSNP: rs2522816079
Type: single nucleotide variant
Location: chrX:71536350 (GRCh38)
Structure: AlphaFold pLDDT 93.41 · 44 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

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OGT p.Lys1010Arg Uncertain significance ★★ ⚠ same condition
OGT p.Lys992Ile Uncertain significance ★★ ⚠ same condition
OGT p.Pro619Leu Uncertain significance ★★ ⚠ same condition
OGT p.Ala169Val Uncertain significance ★ ⚠ same condition
OGT p.Ala259Thr Uncertain significance ★ ⚠ same condition
OGT p.Arg825His Uncertain significance ★ ⚠ same condition
OGT p.Arg899Cys Uncertain significance ★ ⚠ same condition

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/ogt-p-arg70ser (accessed [today's date]).

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