APCDD1 p.Ala160=
c.480C>T · rs3748414 · VCV1282572
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 17.1%, mid) — too common for a highly-penetrant pathogenic allele
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 -8.8 | GERP -4 |
| Overall | ||
| CADD | 0.913 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
17.1%
Middle Eastern · 1,036/6,060 alleles
Filtering AF
16.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 16.2%
Overall
12.2%
196,070/1,612,846 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 17.1% | 6 |
| South Asian | 16.5% | 6 |
| Amishnot grpmax-eligible | 12.9% | 8 |
| East Asian | 12.7% | 8 |
| European (non-Finnish) | 12.6% | 8 |
| Remaining individualsnot grpmax-eligible | 11.9% | 8 |
| Finnishnot grpmax-eligible | 10.4% | 10 |
| Ashkenazi Jewishnot grpmax-eligible | 8.91% | 11 |
| Admixed American | 8.46% | 12 |
| African / African-American | 5.41% | 18 |
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.Ala160=
- Coding
- c.480C>T
- MANE Select
- NM_153000
- dbSNP
- rs3748414
- Type
- single nucleotide variant
- Location
- chr18:10471767 (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-ala160 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown