Is SLC2A1 p.Pro36Arg (c.107C>G) pathogenic?

SLC2A1 p.Pro36Arg (c.107C>G) is classified Likely pathogenic in SLC2A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-22). AlphaMissense: likely pathogenic (0.9772); Absent from gnomAD v4.1; Associated with Seizure.

What condition is associated with SLC2A1 p.Pro36Arg (c.107C>G)?

SLC2A1 p.Pro36Arg (c.107C>G) is associated with Seizure (ClinVar).

How common is SLC2A1 p.Pro36Arg (c.107C>G) in the general population?

SLC2A1 p.Pro36Arg (c.107C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SLC2A1 p.Pro36Arg (c.107C>G)?

AlphaMissense predicts likely pathogenic (score 0.9772) — an in-silico prediction, not a clinical call.

SLC2A1 p.Pro36Arg

c.107C>G · VCV4073672

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9772 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Seizure

Computational evidence

Protein change
AlphaMissense	0.9772	likely pathogenic ✓ concordant with ClinVar
REVEL	0.961	strongly pathogenic-leaning
SaProt	LLR -16.44	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.6, phastCons 1
Regional constraint	o/e 0.55	unconstrained · MANE · 28 kb · p 3.1e-09 · regional, not allelic
Overall
CADD	33.0	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.Pro36Arg
Coding: c.107C>G
MANE Select: NM_006516
Type: single nucleotide variant
Location: chr1:42943233 (GRCh38)
Gene constraint: LOEUF 0.139 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 90.30 · 5 PDB

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

Disease context

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

Similar variants

SLC2A1 p.Pro36Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
SLC2A1 p.Pro36Ser Uncertain significance ★ ⚠ same residue
SLC2A1 p.Pro36Thr Uncertain significance ★ ⚠ same residue
SLC2A1 p.Asn34Ser Pathogenic ★★ same condition
SLC2A1 c.115-2A>C Pathogenic ★★ same type
SLC2A1 c.115-2A>G Pathogenic ★★ same type
SLC2A1 c.1279-2A>G Likely pathogenic ★★ same type
SLC2A1 c.18+1G>A 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/slc2a1-p-pro36arg (accessed [today's date]).

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