APCDD1 p.Pro443=
c.1329C>A · VCV3716082
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
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 0.84 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 7.417 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,028 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.00062%
10/1,614,068 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 20,009 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
| European (non-Finnish) | 0.000508% | 196,675 |
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
- APCDD1
- Protein
- p.Pro443=
- Coding
- c.1329C>A
- MANE Select
- NM_153000
- Type
- single nucleotide variant
- Location
- chr18:10487822 (GRCh38)
- Gene constraint
- LOEUF 0.586 · pLI 0.59 (gnomAD)
- Structure
- AlphaFold pLDDT 82.10
- Residue 443
- the 'disordered' region
Similar variants
- APCDD1 p.Ala176Thr Uncertain significance ★★ ⚠ same type
- APCDD1 p.Ala343Thr Uncertain significance ★★ ⚠ same type
- APCDD1 p.Arg169His Uncertain significance ★★ ⚠ same type
- APCDD1 p.Arg213Gln Uncertain significance ★★ ⚠ same type
- APCDD1 p.Arg303Cys Uncertain significance ★★ ⚠ same type
- APCDD1 p.Arg344Trp Uncertain significance ★★ ⚠ same type
- APCDD1 p.Arg432Gln Uncertain significance ★★ ⚠ same type
- APCDD1 p.Glu393Lys 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/apcdd1-p-pro443 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown