APCDD1 p.Ser273=
c.819A>G · rs61741632 · VCV714868
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.06%, 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 -16 | GERP -4 |
| Overall | ||
| CADD | 0.005 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.06%
African / African-American · 2,300/75,056 alleles
Filtering AF
2.96%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.92%
Overall
0.172%
2,784/1,614,204 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.06% | 33 |
| Remaining individualsnot grpmax-eligible | 0.243% | 411 |
| Middle Eastern | 0.198% | 505 |
| Admixed American | 0.17% | 588 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0405% | 2,467 |
| European (non-Finnish) | 0.017% | 5,871 |
| South Asian | 0.00439% | 22,772 |
| East Asian | 0.00223% | 44,878 |
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.Ser273=
- Coding
- c.819A>G
- MANE Select
- NM_153000
- dbSNP
- rs61741632
- Type
- single nucleotide variant
- Location
- chr18:10485506 (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-ser273 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown