GCK p.Phe330=
c.990C>T · rs773582328 · VCV1256352
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.19 | GERP -1.7, phastCons 0.036 |
| Overall | ||
| CADD | 12.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,080 alleles
Overall
6.87e-05%
1/1,455,302 alleles · very rare
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
- GCK
- Protein
- p.Phe330=
- Coding
- c.990C>T
- MANE Select
- NM_000162
- dbSNP
- rs773582328
- Type
- single nucleotide variant
- Location
- chr7:44146492 (GRCh38)
- Gene constraint
- LOEUF 0.866 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 93.87 · 35 PDB
- Residue 330
- the hexokinase domain; the 'hexokinase large subdomain' region; a UniProt-annotated variant site (in mody2); a UniProt-annotated variant site (in mody2 and t2d)
Similar variants
- GCK p.Phe330Ser Likely pathogenic ★ same residue
- GCK p.Phe330Val Uncertain significance ★ ⚠ same residue
- GCK c.1019+1G>A Pathogenic ★★★ same type
- GCK c.1019+1G>T Pathogenic ★★★ same type
- GCK c.1019+2T>G Pathogenic ★★★ same type
- GCK c.1019+5G>A Likely pathogenic ★★★ same type
- GCK c.1020-10C>A Likely pathogenic ★★★ same type
- GCK c.1020-1G>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/gck-p-phe330 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown