Is DGUOK p.Ser27Phe (c.80C>T) pathogenic?

DGUOK p.Ser27Phe (c.80C>T) is classified Uncertain significance in DGUOK (ClinVar, Single submitter, 1 submitter; last evaluated 2016-10-05). AlphaMissense: likely benign (0.0936); Absent from gnomAD v4.1.

How common is DGUOK p.Ser27Phe (c.80C>T) in the general population?

DGUOK p.Ser27Phe (c.80C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DGUOK p.Ser27Phe (c.80C>T)?

AlphaMissense predicts likely benign (score 0.0936) — an in-silico prediction, not a clinical call.

DGUOK p.Ser27Phe

c.80C>T · rs1300589513 · VCV497803

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0936 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0936	likely benign
REVEL	0.27	benign-leaning
SaProt	LLR -7.60	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 -1.1	GERP -4.2
Regional constraint	o/e 1.07	unconstrained · MANE · 32 kb · p 0.18 · regional, not allelic
Overall
CADD	12.39	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: DGUOK
Protein: p.Ser27Phe
Coding: c.80C>T
MANE Select: NM_080916
dbSNP: rs1300589513
Type: single nucleotide variant
Location: chr2:73926990 (GRCh38)
Gene constraint: LOEUF 1.115 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 87.27 · 1 PDB

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

Similar variants

DGUOK p.Ser27= Likely benign ★ same residue
DGUOK c.443+1G>A Pathogenic ★★ same type
DGUOK c.444-62C>A Pathogenic/Likely pathogenic ★★ same type
DGUOK p.Arg118Cys Pathogenic/Likely pathogenic ★★ same type
DGUOK p.Arg118His Pathogenic/Likely pathogenic ★★ same type
DGUOK p.Arg142Lys Pathogenic/Likely pathogenic ★★ same type
DGUOK p.Asp255Tyr Pathogenic/Likely pathogenic ★★ ⚠ same type
DGUOK p.Gln197= Pathogenic/Likely pathogenic ★★ 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/dguok-p-ser27phe (accessed [today's date]).

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