Is SLC2A1 p.Phe379del (c.1131CTT[1]) pathogenic?

SLC2A1 p.Phe379del (c.1131CTT[1]) is classified Conflicting classifications of pathogenicity in SLC2A1 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-04-28). Absent from gnomAD; Associated with GLUT1 deficiency syndrome 1, autosomal recessive.

What condition is associated with SLC2A1 p.Phe379del (c.1131CTT[1])?

SLC2A1 p.Phe379del (c.1131CTT[1]) is associated with GLUT1 deficiency syndrome 1, autosomal recessive (ClinVar).

How common is SLC2A1 p.Phe379del (c.1131CTT[1]) in the general population?

SLC2A1 p.Phe379del (c.1131CTT[1]) is absent from gnomAD (gnomAD).

SLC2A1 p.Phe379del

c.1131CTT[1] · rs2524984781 · VCV2054084

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

GLUT1 deficiency syndrome 1, autosomal recessive

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.53	GERP 1.9, phastCons 0.82

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SLC2A1
Protein: p.Phe379del
Coding: c.1131CTT[1]
MANE Select: NM_006516
dbSNP: rs2524984781
Type: Microsatellite
Location: chr1:42927747 (GRCh38)
Gene constraint: LOEUF 0.139 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 90.30 · 5 PDB
Residue 379: an α-helix

Full SLC2A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

GLUT1 deficiency syndrome 1, autosomal recessive — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SLC2A1 p.Phe379fs Pathogenic ★ same residue
SLC2A1 p.Ser55fs Pathogenic ★ same condition
SLC2A1 p.Val166del Pathogenic ★ same condition
SLC2A1 p.Val83fs Pathogenic ★ same condition
SLC2A1 c.1279-11_1279-8del Conflicting classifications of pathogenicity ★ same condition
SLC2A1 p.59TTL[1] Uncertain significance ★ same condition
SLC2A1 p.Glu221del Uncertain significance ★ same condition
SLC2A1 p.Leu204del 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/slc2a1-p-phe379del (accessed [today's date]).

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