GCK p.Arg155Ser
c.465G>T · rs757281286 · VCV2628364
ClinGen expert panel — Monogenic Diabetes VCEP
Likely Pathogenic for monogenic diabetes. Applied ACMG criteria (verbatim):
PP4_Moderate PM2_Supporting PP1 PP2 PP3
Curation rationale (ClinGen, verbatim)
The c.465G>T variant in the glucokinase gene, GCK, causes an amino acid change of arginine to serine at codon 155 (p.(Arg155Ser)) of NM_000162.5. GCK is defined by the ClinGen MDEP as a gene that has a low rate of benign missense variation and has pathogenic missense variants as a common mechanism of disease (PP2). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.766, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant segregated with diabetes, with three informative meioses in one family (PP1; internal lab contributors). This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and antibody negative) (PP4_Moderate; internal lab contributors). In summary, c.465G>T meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PM2_Supporting, PP3, PP2, PP1, PP4_Moderate.
ClinGen Evidence Repository → · reported verbatim, not re-tallied by Sugi Variant.
Computational evidence
| Protein change | ||
| AlphaMissense | 0.5056 | ambiguous |
|---|---|---|
| REVEL | 0.766 | pathogenic-leaning |
| SaProt | LLR -7.99 | tolerated |
| ⇒ REVEL calls this damaging; SaProt does not; AlphaMissense makes no call. | ||
| Splicing | ||
| SpliceAI | Δ0.92 | donor gain · deltas |
| Pangolin | Δ0.73 | gain · loss 0.13 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.79 | GERP -2, phastCons 1 |
| Regional constraint | o/e 0.71 | unconstrained · MANE · 7,224 bp · p 1.1e-11 · 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
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
- GCK
- Protein
- p.Arg155Ser
- Coding
- c.465G>T
- MANE Select
- NM_000162
- dbSNP
- rs757281286
- Type
- single nucleotide variant
- Location
- chr7:44150974 (GRCh38)
- Gene constraint
- LOEUF 0.866 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 93.87 · 35 PDB
- Residue 155
- the hexokinase domain; a β-strand; the 'hexokinase small subdomain' region; a UniProt-annotated variant site (in mody2)
Similar variants
- GCK p.Arg155Thr Likely pathogenic ★★★ ⚠ same residue
- GCK p.Arg155Gly Uncertain significance ★★★ ⚠ same residue
- GCK p.Arg155= Likely benign ★ same residue
- GCK c.1019+1G>A Pathogenic ★★★ same condition
- GCK c.1019+1G>T Pathogenic ★★★ same condition
- GCK c.1019+2T>G Pathogenic ★★★ same condition
- GCK c.1019+5G>A Likely pathogenic ★★★ same condition
- GCK c.1020-10C>A 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/gck-p-arg155ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown