COPA p.Tyr982Ser
c.2945A>C · VCV3895906
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.3459 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/2 damaging
REVEL, SaProt · AlphaMissense no call
Computational evidence
| Protein change | ||
| AlphaMissense | 0.3459 | ambiguous |
|---|---|---|
| REVEL | 0.218 | benign-leaning |
| SaProt | LLR -13.47 | damaging |
| ⇒ SaProt calls this damaging; REVEL does not; AlphaMissense makes no call. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 2.8, phastCons 1 |
| Regional constraint | o/e 0.72 | unconstrained · MANE · 42 kb · p 1.1e-24 · regional, not allelic |
| Overall | ||
| CADD | 25.0 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- COPA
- Protein
- p.Tyr982Ser
- Coding
- c.2945A>C
- MANE Select
- NM_004371
- Type
- single nucleotide variant
- Location
- chr1:160292499 (GRCh38)
- Gene constraint
- LOEUF 0.098 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.85 · 3 PDB
Similar variants
- COPA p.Arg233His Pathogenic/Likely pathogenic ★★ same type
- COPA p.Glu241Lys Pathogenic ★★ same type
- COPA p.Ala111Thr Uncertain significance ★★ ⚠ same type
- COPA p.Ala176Val Uncertain significance ★★ ⚠ same type
- COPA p.Ala407Val Uncertain significance ★★ ⚠ same type
- COPA p.Ala422Thr Uncertain significance ★★ ⚠ same type
- COPA p.Ala469Val Uncertain significance ★★ ⚠ same type
- COPA p.Ala510Thr 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/copa-p-tyr982ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown