CDH2 p.Thr10=
c.30C>A · rs2510801327 · VCV1727600
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,474,622)
Conditions
1
Inborn genetic diseases
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 7.7 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 15.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,474,622). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CDH2
- Protein
- p.Thr10=
- Coding
- c.30C>A
- MANE Select
- NM_001792
- dbSNP
- rs2510801327
- Type
- single nucleotide variant
- Location
- chr18:28176993 (GRCh38)
- Gene constraint
- LOEUF 0.336 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.68
Similar variants
- CDH2 p.Thr10Ala Uncertain significance ★★ ⚠ same residue
- CDH2 p.Thr10Asn Uncertain significance ★★ ⚠ same residue
- CDH2 p.Thr10Ile Uncertain significance ★★ ⚠ same residue
- CDH2 p.Thr10Pro Uncertain significance ★★ ⚠ same residue
- CDH2 p.Thr10Ser Uncertain significance ★★ ⚠ same residue
- CDH2 p.Ala21Val Uncertain significance ★★ ⚠ same condition
- CDH2 p.Ala294Gly Uncertain significance ★★ ⚠ same condition
- CDH2 p.Ala299Thr Uncertain significance ★★ ⚠ same condition
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/cdh2-p-thr10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown