CDCP1 p.Ala306=
c.918G>A · rs12634943 · VCV773572
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.18%, eas)
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 -5.7 | GERP -4.3 |
| Overall | ||
| CADD | 1.185 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.18%
East Asian · 1,428/44,882 alleles
Filtering AF
3.04%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.99%
Overall
0.286%
4,617/1,614,154 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 3.18% | 31 |
| African / African-American | 1.96% | 51 |
| Remaining individualsnot grpmax-eligible | 0.394% | 254 |
| South Asian | 0.186% | 539 |
| Middle Eastern | 0.132% | 758 |
| Admixed American | 0.127% | 790 |
| European (non-Finnish) | 0.103% | 970 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,802 |
| Finnishnot grpmax-eligible | 0.00625% | 16,009 |
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
- CDCP1
- Protein
- p.Ala306=
- Coding
- c.918G>A
- MANE Select
- NM_022842
- dbSNP
- rs12634943
- Type
- single nucleotide variant
- Location
- chr3:45110579 (GRCh38)
- Gene constraint
- LOEUF 0.601 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 78.13
Similar variants
- CDCP1 p.Arg763Gln Benign ★★ same type
- CDCP1 p.Gly596Ser Benign ★★ ⚠ same type
- CDCP1 p.Ala212Val Uncertain significance ★ ⚠ same type
- CDCP1 p.Ala320Thr Uncertain significance ★ ⚠ same type
- CDCP1 p.Ala464Gly Uncertain significance ★ ⚠ same type
- CDCP1 p.Ala521Gly Uncertain significance ★ ⚠ same type
- CDCP1 p.Ala528Ser Uncertain significance ★ ⚠ same type
- CDCP1 p.Ala604Thr 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/cdcp1-p-ala306 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown