CDC14A p.Leu264=
c.792G>C · rs764506271 · VCV2900286
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00449%, 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 3.2 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 16.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00449%
European (non-Finnish) · 53/1,180,004 alleles
Filtering AF
0.0035%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00318%
Overall
0.00341%
55/1,613,864 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00449% | 22,264 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,241 |
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.Leu264=
- Coding
- c.792G>C
- MANE Select
- NM_003672
- dbSNP
- rs764506271
- Type
- single nucleotide variant
- Location
- chr1:100462835 (GRCh38)
- Gene constraint
- LOEUF 1.141 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.77
- Residue 264
- the tyrosine-protein phosphatase domain; a UniProt-annotated variant site (in dfnb32); the 'b' region
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-leu264 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown