CDC14A p.Thr570=
c.1710C>T · rs758911240 · VCV2889222
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0869%, eas)
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 -8.9 | GERP -4.7 |
| Overall | ||
| CADD | 3.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0869%
East Asian · 39/44,886 alleles
Filtering AF
0.0653%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0578%
Overall
0.0039%
63/1,614,194 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0869% | 1,151 |
| Admixed American | 0.00333% | 30,012 |
| European (non-Finnish) | 0.00161% | 62,108 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
| African / African-American | 0.00133% | 75,050 |
| South Asian | 0.0011% | 91,074 |
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
- CDC14A
- Protein
- p.Thr570=
- Coding
- c.1710C>T
- MANE Select
- NM_003672
- dbSNP
- rs758911240
- Type
- single nucleotide variant
- Location
- chr1:100499217 (GRCh38)
- Gene constraint
- LOEUF 1.141 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.77
- Residue 570
- a UniProt-annotated variant site (in dfnb32)
Similar variants
- CDC14A p.Arg261Ter Pathogenic ★★ same type
- CDC14A p.Arg312Gln Pathogenic/Likely pathogenic ★★ same type
- CDC14A p.Arg312Gly Pathogenic/Likely pathogenic ★★ same type
- CDC14A p.Arg339Ter Pathogenic ★★ same type
- CDC14A p.Arg345Ter Pathogenic/Likely pathogenic ★★ same type
- CDC14A p.Arg376Ter Pathogenic/Likely pathogenic ★★ same type
- CDC14A p.Ala211Gly Uncertain significance ★★ ⚠ same type
- CDC14A p.Ala482Thr 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/cdc14a-p-thr570 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown