GCGR p.Arg417=
c.1251C>T · rs61738411 · VCV726818
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.43%, 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 -2.4 |
| Overall | ||
| CADD | 3.868 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.43%
African / African-American · 1,045/73,134 alleles
Filtering AF
1.36%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.33%
Overall
0.0761%
1,169/1,535,676 alleles · low-frequency
exomes 581/1,383,422 · genomes 588/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.43% | 70 |
| Remaining individualsnot grpmax-eligible | 0.11% | 909 |
| Admixed American | 0.0608% | 1,645 |
| Middle Eastern | 0.0349% | 2,867 |
| European (non-Finnish) | 0.00209% | 47,782 |
| South Asian | 0.00119% | 84,044 |
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.Arg417=
- Coding
- c.1251C>T
- MANE Select
- NM_000160
- dbSNP
- rs61738411
- Type
- single nucleotide variant
- Location
- chr17:81813506 (GRCh38)
- Gene constraint
- LOEUF 1.018 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.56 · 28 PDB
- Residue 417
- an α-helix
Similar variants
- GCGR p.Arg417His Uncertain significance ★★ ⚠ same residue
- GCGR p.Arg417Cys Uncertain significance ★ ⚠ same residue
- 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.Leu358Val Uncertain significance ★★ ⚠ same type
- GCGR p.Phe181Ser 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-arg417 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown