COPS2 p.Pro301=
c.903G>A · rs148364582 · VCV788586
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.09%, 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 -0.71 | GERP -0.63, phastCons 0.003 |
| Overall | ||
| CADD | 12.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.09%
African / African-American · 803/73,958 alleles
Filtering AF
1.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.999%
Overall
0.056%
894/1,597,404 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.09% | 92 |
| Remaining individualsnot grpmax-eligible | 0.0534% | 1,874 |
| Admixed American | 0.0477% | 2,096 |
| East Asian | 0.00448% | 22,303 |
| European (non-Finnish) | 0.00239% | 41,925 |
| Finnishnot grpmax-eligible | 0.00157% | 63,694 |
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
- COPS2
- Protein
- p.Pro301=
- Coding
- c.903G>A
- MANE Select
- NM_004236
- dbSNP
- rs148364582
- Type
- single nucleotide variant
- Location
- chr15:49133803 (GRCh38)
- Gene constraint
- LOEUF 0.138 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.22 · 29 PDB
- Residue 301
- the pci domain
Similar variants
- COPS2 p.Pro47= Likely benign ★★ same type
- COPS2 p.Ala419Gly Uncertain significance ★ ⚠ same type
- COPS2 p.Ala419Thr Uncertain significance ★ ⚠ same type
- COPS2 p.Ala49Val Uncertain significance ★ ⚠ same type
- COPS2 p.Arg162Gln Uncertain significance ★ ⚠ same type
- COPS2 p.Arg401Gln Uncertain significance ★ ⚠ same type
- COPS2 p.Arg416Gly Uncertain significance ★ ⚠ same type
- COPS2 p.Arg420Gln 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/cops2-p-pro301 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown