COPS2 p.Pro47=
c.141A>T · rs372953422 · VCV761853
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.389%, mid)
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 -0.034 | GERP 3.4, phastCons 0.92 |
| Overall | ||
| CADD | 10.31 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.389%
Middle Eastern · 23/5,914 alleles
Filtering AF
0.266%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.225%
Overall
0.0117%
187/1,595,656 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.389% | 257 |
| Remaining individualsnot grpmax-eligible | 0.0227% | 4,409 |
| European (non-Finnish) | 0.0118% | 8,503 |
| Admixed American | 0.00896% | 11,162 |
| South Asian | 0.00689% | 14,520 |
| African / African-American | 0.00136% | 73,732 |
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.Pro47=
- Coding
- c.141A>T
- MANE Select
- NM_004236
- dbSNP
- rs372953422
- Type
- single nucleotide variant
- Location
- chr15:49144992 (GRCh38)
- Gene constraint
- LOEUF 0.138 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.22 · 29 PDB
- Residue 47
- an α-helix; the 'mediates interaction with nif3l1' region
Similar variants
- 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
- COPS2 p.Asn304Ser 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-pro47 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown