CDON p.Thr630=
c.1890G>C · rs142039749 · VCV916400
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.081 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -3.8 |
| Overall | ||
| CADD | 0.254 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,826 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000205%
3/1,461,808 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,826 |
| European (non-Finnish) | 0.000169% | 589,998 |
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
- CDON
- Protein
- p.Thr630=
- Coding
- c.1890G>C
- MANE Select
- NM_001378964
- dbSNP
- rs142039749
- Type
- single nucleotide variant
- Location
- chr11:126004038 (GRCh38)
- Gene constraint
- LOEUF 0.733 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.62 · 3 PDB
- Residue 630
- the fibronectin type-iii 1 domain
Similar variants
- CDON p.Thr630Met Likely benign ★★ ⚠ same residue
- CDON c.3276+1G>T Uncertain significance ★★ same type
- CDON c.640+1G>A Uncertain significance ★★ same type
- CDON c.*1805A>G Uncertain significance ★★ same type
- CDON c.*1816C>T Uncertain significance ★★ same type
- CDON c.*2349A>C Uncertain significance ★★ same type
- CDON c.*2377T>C Uncertain significance ★★ same type
- CDON c.*2760A>G 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/cdon-p-thr630 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown