COPG1 p.Ile357=
c.1071C>T · VCV3387905
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.805%, eas)
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 -9.8 | GERP -3.7 |
| Overall | ||
| CADD | 2.897 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.805%
East Asian · 361/44,872 alleles
Filtering AF
0.736%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.709%
Overall
0.234%
3,767/1,613,002 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.805% | 124 |
| South Asian | 0.757% | 132 |
| African / African-American | 0.508% | 197 |
| Middle Eastern | 0.348% | 287 |
| Remaining individualsnot grpmax-eligible | 0.269% | 371 |
| European (non-Finnish) | 0.172% | 583 |
| Admixed American | 0.165% | 606 |
| Finnishnot grpmax-eligible | 0.0297% | 3,370 |
| Ashkenazi Jewishnot grpmax-eligible | 0.027% | 3,701 |
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
- COPG1
- Protein
- p.Ile357=
- Coding
- c.1071C>T
- MANE Select
- NM_016128
- Type
- single nucleotide variant
- Location
- chr3:129260750 (GRCh38)
- Gene constraint
- LOEUF 0.376 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 88.09 · 1 PDB
Similar variants
- COPG1 p.Arg247His Uncertain significance ★★ ⚠ same type
- COPG1 p.Leu864Met Uncertain significance ★★ ⚠ same type
- COPG1 p.Thr64Met Uncertain significance ★★ ⚠ same type
- COPG1 c.91-11T>C Benign ★★ same type
- COPG1 c.939+13C>G Benign ★★ same type
- COPG1 p.His221= Benign ★★ same type
- COPG1 p.Ile92= Benign/Likely benign ★★ same type
- COPG1 p.Leu240Val Benign/Likely benign ★★ ⚠ 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/copg1-p-ile357 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown