CDCP2 p.Tyr202=
c.606C>T · VCV3998739
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00799%, 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 -7.7 | GERP -4.2 |
| Overall | ||
| CADD | 1.274 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00799%
African / African-American · 6/75,080 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00228%
Overall
0.00198%
32/1,614,224 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00799% | 12,513 |
| East Asian | 0.00446% | 22,442 |
| Admixed American | 0.00333% | 30,006 |
| European (non-Finnish) | 0.00178% | 56,192 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
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
- CDCP2
- Protein
- p.Tyr202=
- Coding
- c.606C>T
- MANE Select
- NM_001353655
- Type
- single nucleotide variant
- Location
- chr1:54141255 (GRCh38)
- Gene constraint
- LOEUF 1.369 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.43
- Residue 202
- a disulfide bond; the cub 2 domain
Similar variants
- CDCP2 c.1117+105C>T Uncertain significance ★ ⚠ same type
- CDCP2 c.1117+106C>T Uncertain significance ★ ⚠ same type
- CDCP2 c.1117+10G>A Uncertain significance ★ ⚠ same type
- CDCP2 c.1117+110G>T Uncertain significance ★ ⚠ same type
- CDCP2 c.1117+15G>A Uncertain significance ★ ⚠ same type
- CDCP2 c.1117+168C>G Uncertain significance ★ ⚠ same type
- CDCP2 c.1117+184C>T Uncertain significance ★ ⚠ same type
- CDCP2 c.1117+97C>T 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/cdcp2-p-tyr202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown