CDC14A p.Gly157=
c.471A>C · rs138318034 · VCV1649383
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0895%, 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 2.2 | GERP 0.6, phastCons 1 |
| Overall | ||
| CADD | 9.347 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0895%
East Asian · 40/44,690 alleles
Filtering AF
0.0676%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0598%
Overall
0.00274%
44/1,603,190 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0895% | 1,117 |
| Remaining individualsnot grpmax-eligible | 0.00322% | 31,058 |
| Admixed American | 0.00167% | 59,870 |
| South Asian | 0.0011% | 90,744 |
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.Gly157=
- Coding
- c.471A>C
- MANE Select
- NM_003672
- dbSNP
- rs138318034
- Type
- single nucleotide variant
- Location
- chr1:100442948 (GRCh38)
- Gene constraint
- LOEUF 1.141 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.77
- Residue 157
- a UniProt-annotated variant site (in dfnb32); the 'a' 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-gly157 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown