Is OGT p.Pro52Ser (c.154C>T) pathogenic?

OGT p.Pro52Ser (c.154C>T) is classified Uncertain significance in OGT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-20). AlphaMissense: likely benign (0.26); Absent from gnomAD v4.1.

How common is OGT p.Pro52Ser (c.154C>T) in the general population?

OGT p.Pro52Ser (c.154C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about OGT p.Pro52Ser (c.154C>T)?

AlphaMissense predicts likely benign (score 0.26) — an in-silico prediction, not a clinical call.

OGT p.Pro52Ser

c.154C>T · VCV4086727

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.26 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.26	likely benign
REVEL	0.535	indeterminate
SaProt	LLR -9.77	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.5, phastCons 1
Regional constraint	o/e 0.32	constrained · MANE · 4,749 bp · p 2.7e-13 · regional, not allelic
Overall
CADD	25.5	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

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.Pro52Ser
Coding: c.154C>T
MANE Select: NM_181672
Type: single nucleotide variant
Location: chrX:71536294 (GRCh38)
Structure: AlphaFold pLDDT 93.41 · 44 PDB

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

Similar variants

OGT p.Thr932Ile Likely pathogenic ★★ same type
OGT p.Ala765Thr Uncertain significance ★★ ⚠ same type
OGT p.Arg117Cys Uncertain significance ★★ same type
OGT p.Arg485Gln Uncertain significance ★★ ⚠ same type
OGT p.Arg555Trp Uncertain significance ★★ ⚠ same type
OGT p.Arg627Cys Uncertain significance ★★ ⚠ same type
OGT p.Arg899His Uncertain significance ★★ ⚠ same type
OGT p.Asn898Ser 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/ogt-p-pro52ser (accessed [today's date]).

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