COPG1 p.Lys414=
c.1242G>A · VCV4689134
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 8.23%, afr) — too common for a highly-penetrant pathogenic allele
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 2.5 | GERP 0.8, phastCons 1 |
| Overall | ||
| CADD | 7.123 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.23%
African / African-American · 6,173/75,024 alleles
Filtering AF
8.06%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.99%
Overall
0.491%
7,919/1,614,162 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.23% | 12 |
| Admixed American | 1.04% | 96 |
| Remaining individualsnot grpmax-eligible | 0.755% | 132 |
| Middle Eastern | 0.412% | 242 |
| Ashkenazi Jewishnot grpmax-eligible | 0.25% | 400 |
| European (non-Finnish) | 0.0453% | 2,206 |
| South Asian | 0.0187% | 5,358 |
| East Asian | 0.00223% | 44,884 |
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.Lys414=
- Coding
- c.1242G>A
- MANE Select
- NM_016128
- Type
- single nucleotide variant
- Location
- chr3:129265566 (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-lys414 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown