COPZ1 p.Thr159=
c.477C>A · rs115975751 · VCV746724
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.475%, afr)
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 -11 | GERP -3.9 |
| Overall | ||
| CADD | 0.243 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.475%
African / African-American · 356/75,000 alleles
Filtering AF
0.434%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.418%
Overall
0.0274%
442/1,612,518 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.475% | 211 |
| Middle Eastern | 0.099% | 1,010 |
| Admixed American | 0.06% | 1,668 |
| Remaining individualsnot grpmax-eligible | 0.0544% | 1,837 |
| South Asian | 0.0011% | 91,040 |
| European (non-Finnish) | 0.000764% | 130,946 |
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
- COPZ1
- Protein
- p.Thr159=
- Coding
- c.477C>A
- MANE Select
- NM_016057
- dbSNP
- rs115975751
- Type
- single nucleotide variant
- Location
- chr12:54349649 (GRCh38)
- Gene constraint
- LOEUF 0.443 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 89.37 · 2 PDB
- Residue 159
- a UniProt-annotated variant site (in scn12; likely pathogenic; results in decreased differentiation of neutrophils when expressed in pluripotent stem cells; results in loss of retrograde golgi-to-er transport)
Similar variants
- COPZ1 p.Ala167Thr Uncertain significance ★ ⚠ same type
- COPZ1 p.Ala43Val Uncertain significance ★ ⚠ same type
- COPZ1 p.Arg112Gln Uncertain significance ★ ⚠ same type
- COPZ1 p.Arg145Gln Uncertain significance ★ ⚠ same type
- COPZ1 p.Arg145Trp Uncertain significance ★ ⚠ same type
- COPZ1 p.Arg25Gln Uncertain significance ★ ⚠ same type
- COPZ1 p.Asn21Lys Uncertain significance ★ ⚠ same type
- COPZ1 p.Asp138His 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/copz1-p-thr159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown