APCDD1 p.Thr170=
c.510A>G · rs370392635 · VCV2698605
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.017%, nfe)
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 -8.3 | GERP -4 |
| Overall | ||
| CADD | 0.152 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.017%
European (non-Finnish) · 201/1,179,642 alleles
Filtering AF
0.0151%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0143%
Overall
0.0133%
214/1,613,332 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.017% | 5,869 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,492 |
| African / African-American | 0.00667% | 14,984 |
| Finnishnot grpmax-eligible | 0.0047% | 21,263 |
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.Thr170=
- Coding
- c.510A>G
- MANE Select
- NM_153000
- dbSNP
- rs370392635
- Type
- single nucleotide variant
- Location
- chr18:10471797 (GRCh38)
- Gene constraint
- LOEUF 0.586 · pLI 0.59 (gnomAD)
- Structure
- AlphaFold pLDDT 82.10
Similar variants
- APCDD1 p.Thr170Ile Uncertain significance ★ ⚠ same residue
- 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
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-thr170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown