CDC14A p.Phe249del
c.742TTC[1] · VCV4072595
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.9 | GERP 2.4, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,024 alleles
Overall
6.84e-05%
1/1,461,808 alleles · very rare
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.Phe249del
- Coding
- c.742TTC[1]
- MANE Select
- NM_003672
- Type
- Microsatellite
- Location
- chr1:100462783 (GRCh38)
- Gene constraint
- LOEUF 1.141 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.77
- Residue 249
- the tyrosine-protein phosphatase domain; a UniProt-annotated variant site (in dfnb32); the 'b' region
Similar variants
- CDC14A p.Phe249Leu Uncertain significance ★ ⚠ same residue
- CDC14A p.Ser576del Uncertain significance ★ same type
- CDC14A c.1299-159_1299-158del 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/cdc14a-p-phe249del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown