CDH10 p.Leu625=
c.1875G>A · rs184571175 · VCV2655375
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0307%, 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 -0.2 | GERP -0.71, phastCons 0.38 |
| Overall | ||
| CADD | 8.848 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0307%
African / African-American · 23/74,902 alleles
Filtering AF
0.021%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0178%
Overall
0.00211%
34/1,609,760 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0307% | 3,257 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,924 |
| South Asian | 0.00111% | 90,470 |
| European (non-Finnish) | 8.49e-05% | 1,177,270 |
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
- CDH10
- Protein
- p.Leu625=
- Coding
- c.1875G>A
- MANE Select
- NM_006727
- dbSNP
- rs184571175
- Type
- single nucleotide variant
- Location
- chr5:24491577 (GRCh38)
- Gene constraint
- LOEUF 0.655 · pLI 0.18 (gnomAD)
- Structure
- AlphaFold pLDDT 78.29
Similar variants
- CDH10 p.Met316Ile Uncertain significance ★★ ⚠ same type
- CDH10 p.Thr159Met Uncertain significance ★★ ⚠ same type
- CDH10 p.Glu469= Benign ★★ same type
- CDH10 p.Gly673= Benign ★★ same type
- CDH10 p.Ala296Thr Uncertain significance ★ ⚠ same type
- CDH10 p.Ala501Val Uncertain significance ★ ⚠ same type
- CDH10 p.Ala530Val Uncertain significance ★ ⚠ same type
- CDH10 p.Arg128Cys 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/cdh10-p-leu625 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown