CDH13 p.Asn472=
c.1416C>T · rs147140848 · VCV779363
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.53%, 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 -8.4 | GERP -4.5 |
| Overall | ||
| CADD | 5.88 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.53%
European (non-Finnish) · 18,076/1,179,886 alleles
Filtering AF
1.51%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.51%
Overall
1.23%
19,906/1,613,976 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.53% | 65 |
| Ashkenazi Jewishnot grpmax-eligible | 1.12% | 89 |
| Remaining individualsnot grpmax-eligible | 1.07% | 93 |
| Finnishnot grpmax-eligible | 0.501% | 199 |
| Admixed American | 0.372% | 269 |
| African / African-American | 0.229% | 436 |
| South Asian | 0.123% | 813 |
| Middle Eastern | 0.0165% | 6,062 |
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
- CDH13
- Protein
- p.Asn472=
- Coding
- c.1416C>T
- MANE Select
- NM_001257
- dbSNP
- rs147140848
- Type
- single nucleotide variant
- Location
- chr16:83678339 (GRCh38)
- Gene constraint
- LOEUF 0.456 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.19 · 1 PDB
- Residue 472
- the cadherin 3 domain
Similar variants
- CDH13 p.Asn472Ser Uncertain significance ★ ⚠ same residue
- CDH13 c.1102-6T>C Benign ★★ same type
- CDH13 c.1284+90A>G Benign ★★ same type
- CDH13 c.1539-109T>C Benign ★★ same type
- CDH13 c.1681+64T>C Benign ★★ same type
- CDH13 c.1682-151C>T Benign ★★ same type
- CDH13 c.1682-180G>A Benign ★★ same type
- CDH13 c.1682-59A>G Benign ★★ 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/cdh13-p-asn472 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown