APCDD1 p.Ala63=
c.189A>C · rs35079028 · VCV2046512
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.605%, 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 -9.6 | GERP -4 |
| Overall | ||
| CADD | 0.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.605%
African / African-American · 454/75,054 alleles
Filtering AF
0.559%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.541%
Overall
0.0344%
556/1,614,076 alleles · rare
exomes 295/1,461,756 · genomes 261/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.605% | 165 |
| Middle Eastern | 0.135% | 743 |
| Remaining individualsnot grpmax-eligible | 0.0624% | 1,602 |
| Admixed American | 0.0466% | 2,144 |
| South Asian | 0.00329% | 30,357 |
| European (non-Finnish) | 0.00203% | 49,168 |
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.Ala63=
- Coding
- c.189A>C
- MANE Select
- NM_153000
- dbSNP
- rs35079028
- Type
- single nucleotide variant
- Location
- chr18:10468599 (GRCh38)
- Gene constraint
- LOEUF 0.586 · pLI 0.59 (gnomAD)
- Structure
- AlphaFold pLDDT 82.10
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-ala63 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown