Is SLC2A1 p.Ser313= (c.939C>T) pathogenic?

SLC2A1 p.Ser313= (c.939C>T) is classified Likely benign in SLC2A1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-09-09). Ultra-rare (popmax 0.0164%, mid); Associated with dystonia 9.

How common is SLC2A1 p.Ser313= (c.939C>T) in the general population?

SLC2A1 p.Ser313= (c.939C>T) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

SLC2A1 p.Ser313=

Q: What condition is associated with SLC2A1 p.Ser313= (c.939C>T)?

SLC2A1 p.Ser313= (c.939C>T) is associated with dystonia 9, encephalopathy due to GLUT1 deficiency, hereditary cryohydrocytosis with reduced stomatin (ClinVar).

Q: How is Paroxysmal dystonic choreathetosis with episodic ataxia and spasticity inherited?

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

c.939C>T · rs775408842 · VCV697940

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Conditions

dystonia 9

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.46 · evaluated, not missing
Constraint at this position
Conservation	phyloP -8.2	GERP -3.7
Overall
CADD	6.689	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,084 alleles

Filtering AF 0.00726% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00514%

Overall 0.00211% 34/1,613,956 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,084
East Asian	0.0156%	6,412
African / African-American	0.00934%	10,702
South Asian	0.00549%	18,215
Remaining individualsnot grpmax-eligible	0.0016%	62,480
European (non-Finnish)	0.0011%	90,768

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: SLC2A1
Protein: p.Ser313=
Coding: c.939C>T
MANE Select: NM_006516
dbSNP: rs775408842
Type: single nucleotide variant
Location: chr1:42929243 (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

dystonia 9 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: encephalopathy due to GLUT1 deficiency hereditary cryohydrocytosis with reduced stomatin childhood onset GLUT1 deficiency syndrome 2 epilepsy, idiopathic generalized, susceptibility to, 12

For Paroxysmal dystonic choreathetosis with episodic ataxia and spasticity (Orphanet):

Inheritance: Autosomal dominant
Onset: Childhood

Similar variants

SLC2A1 p.Ser313Phe Likely pathogenic ★ same residue
SLC2A1 p.Ser313Pro Conflicting classifications of pathogenicity ★ ⚠ same residue
SLC2A1 p.Ser313Tyr Uncertain significance ★ ⚠ same residue
SLC2A1 c.115-2A>C Pathogenic ★★ same condition
SLC2A1 c.115-2A>G Pathogenic ★★ same condition
SLC2A1 c.18+1G>A Pathogenic ★★ same condition
SLC2A1 c.19-2A>G Pathogenic ★★ same condition
SLC2A1 c.275+1G>C 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-ser313 (accessed [today's date]).

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