Is SLC2A1 p.Ser313Phe (c.938C>T) pathogenic?

SLC2A1 p.Ser313Phe (c.938C>T) is classified Likely pathogenic in SLC2A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2014-12-11). AlphaMissense: likely pathogenic (0.9019); Absent from gnomAD v4.1; Associated with childhood onset GLUT1 deficiency syndrome 2.

What condition is associated with SLC2A1 p.Ser313Phe (c.938C>T)?

SLC2A1 p.Ser313Phe (c.938C>T) is associated with childhood onset GLUT1 deficiency syndrome 2 (ClinVar).

How common is SLC2A1 p.Ser313Phe (c.938C>T) in the general population?

SLC2A1 p.Ser313Phe (c.938C>T) is absent from gnomAD v4.1 (gnomAD).

How is Paroxysmal exertion-induced dyskinesia inherited?

Typically Autosomal dominant, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about SLC2A1 p.Ser313Phe (c.938C>T)?

AlphaMissense predicts likely pathogenic (score 0.9019) — an in-silico prediction, not a clinical call.

SLC2A1 p.Ser313Phe

c.938C>T · rs794727870 · VCV224104

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9019 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

childhood onset GLUT1 deficiency syndrome 2

Computational evidence

Protein change
AlphaMissense	0.9019	likely pathogenic ✓ concordant with ClinVar
REVEL	0.331	indeterminate
SaProt	LLR -11.01	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Regional constraint	o/e 0.59	unconstrained · MANE · 2,860 bp · p 1.1e-11 · regional, not allelic
Overall
CADD	25.5	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: SLC2A1
Protein: p.Ser313Phe
Coding: c.938C>T
MANE Select: NM_006516
dbSNP: rs794727870
Type: single nucleotide variant
Location: chr1:42929244 (GRCh38)
Gene constraint: LOEUF 0.139 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 90.30 · 5 PDB
Residue 313: an α-helix

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

Disease context

childhood onset GLUT1 deficiency syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Paroxysmal exertion-induced dyskinesia (Orphanet):

Inheritance: Autosomal dominant, Not applicable
Onset: Adolescent, Adult, Childhood, Infancy

Similar variants

SLC2A1 p.Ser313= Likely benign ★★ same residue
SLC2A1 p.Ser313Pro Conflicting classifications of pathogenicity ★ ⚠ same residue
SLC2A1 p.Ser313Tyr Uncertain significance ★ ⚠ same residue
SLC2A1 c.19-2A>G Pathogenic ★★ same condition
SLC2A1 p.Ala275Thr Pathogenic/Likely pathogenic ★★ same condition
SLC2A1 p.Arg126Cys Pathogenic/Likely pathogenic ★★ same condition
SLC2A1 p.Arg126His Pathogenic/Likely pathogenic ★★ same condition
SLC2A1 p.Arg153Cys 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/slc2a1-p-ser313phe (accessed [today's date]).

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