Is GNE p.Phe13= (c.39T>C) pathogenic?

GNE p.Phe13= (c.39T>C) is classified Likely benign in GNE (ClinVar, Single submitter, 1 submitter; last evaluated 2021-03-24). Absent from gnomAD v4.1; Associated with sialuria.

What condition is associated with GNE p.Phe13= (c.39T>C)?

GNE p.Phe13= (c.39T>C) is associated with sialuria, GNE myopathy (ClinVar).

How common is GNE p.Phe13= (c.39T>C) in the general population?

GNE p.Phe13= (c.39T>C) is absent from gnomAD v4.1 (gnomAD).

How is Sialuria inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

GNE p.Phe13=

c.39T>C · rs2133208583 · VCV1543823

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

sialuria

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.022	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.039	GERP -3.3
Overall
CADD	5.551	PHRED · no single calibrated threshold — expert panels disagree

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: GNE
Protein: p.Phe13=
Coding: c.39T>C
MANE Select: NM_005476 · reported on NM_001128227
dbSNP: rs2133208583
Type: single nucleotide variant
Location: chr9:36276906 (GRCh38)
Gene constraint: LOEUF 0.821 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.96 · 5 PDB
Residue 13: a β-strand; a UniProt-annotated variant site (in nm; decreased udp-n-acetylglucosamine 2-epimerase activity; no effect on n-acylmannosamine kinase activity)

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

Disease context

sialuria — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: GNE myopathy

For Sialuria (Orphanet):

Inheritance: Autosomal dominant
Onset: Infancy

Similar variants

GNE p.Cys13Ser Pathogenic ★★ same residue
GNE c.1816+2T>C Pathogenic/Likely pathogenic ★★ same condition
GNE c.1816+5G>A Pathogenic ★★ same condition
GNE c.617-1G>A Likely pathogenic ★★ same condition
GNE c.617-2A>G Pathogenic/Likely pathogenic ★★ same condition
GNE c.982+2T>A Likely pathogenic ★★ same condition
GNE p.Ala524Val Pathogenic/Likely pathogenic ★★ same condition
GNE p.Ala630Thr Pathogenic/Likely pathogenic ★★ 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/gne-p-phe13 (accessed [today's date]).

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