GCGR p.Phe383=
c.1149C>T · rs546540436 · VCV2895900
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.105%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 12.56 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.105%
African / African-American · 77/73,158 alleles
Filtering AF
0.0863%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0793%
Overall
0.00605%
93/1,536,074 alleles · rare
exomes 37/1,383,742 · genomes 56/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.105% | 950 |
| Admixed American | 0.0176% | 5,666 |
| Remaining individualsnot grpmax-eligible | 0.01% | 10,002 |
| South Asian | 0.00119% | 84,052 |
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
- GCGR
- Protein
- p.Phe383=
- Coding
- c.1149C>T
- MANE Select
- NM_000160
- dbSNP
- rs546540436
- Type
- single nucleotide variant
- Location
- chr17:81812918 (GRCh38)
- Gene constraint
- LOEUF 1.018 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.56 · 28 PDB
- Residue 383
- an α-helix
Similar variants
- GCGR p.Ala373Thr Uncertain significance ★★ ⚠ same type
- GCGR p.Ala380Thr Uncertain significance ★★ ⚠ same type
- GCGR p.Arg324Cys Uncertain significance ★★ ⚠ same type
- GCGR p.Arg413Gln Uncertain significance ★★ ⚠ same type
- GCGR p.Arg417His Uncertain significance ★★ ⚠ same type
- GCGR p.Leu358Val Uncertain significance ★★ ⚠ same type
- GCGR p.Phe181Ser Uncertain significance ★★ ⚠ same type
- GCGR p.Pro52Thr Uncertain significance ★★ ⚠ 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/gcgr-p-phe383 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown