GCGR p.Ser48=
c.144C>T · rs980081455 · VCV3047477
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00933%, nfe)
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 1.6 | GERP 0.9, phastCons 1 |
| Overall | ||
| CADD | 12.41 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00933%
European (non-Finnish) · 107/1,146,754 alleles
Filtering AF
0.00788%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00729%
Overall
0.00723%
111/1,536,296 alleles · very rare
exomes 104/1,384,054 · genomes 7/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00933% | 10,717 |
| Remaining individualsnot grpmax-eligible | 0.005% | 19,999 |
| African / African-American | 0.00137% | 73,044 |
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.Ser48=
- Coding
- c.144C>T
- MANE Select
- NM_000160
- dbSNP
- rs980081455
- Type
- single nucleotide variant
- Location
- chr17:81809865 (GRCh38)
- Gene constraint
- LOEUF 1.018 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.56 · 28 PDB
- Residue 48
- 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-ser48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown