PLK4 p.Pro679=
c.2037A>G · rs775938135 · VCV1449123
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00146%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.31 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.23 | loss · gain 0.15 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 4.9 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 17.93 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00146%
African / African-American · 1/68,496 alleles
Filtering AF
3.4e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.3e-05%
Overall
0.000224%
3/1,341,366 alleles · very rare
exomes 3/1,189,442 · genomes 0/151,924 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00146% | 68,496 |
| European (non-Finnish) | 0.000203% | 493,274 |
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
- PLK4
- Protein
- p.Pro679=
- Coding
- c.2037A>G
- MANE Select
- NM_014264
- dbSNP
- rs775938135
- Type
- single nucleotide variant
- Location
- chr4:127891680 (GRCh38)
- Gene constraint
- LOEUF 0.619 · pLI 0.18 (gnomAD)
- Structure
- AlphaFold pLDDT 66.31 · 19 PDB
- Residue 679
- the cryptic polo box 1 (cpb1) domain
Similar variants
- PLK4 p.Pro679Arg Uncertain significance ★ ⚠ same residue
- PLK4 c.1358+1G>C Likely pathogenic ★★ same type
- PLK4 p.Arg185Ter Pathogenic/Likely pathogenic ★★ same type
- PLK4 c.126+5G>C Uncertain significance ★★ same type
- PLK4 c.1935+4A>T Uncertain significance ★★ same type
- PLK4 p.Arg185Gln Uncertain significance ★★ same type
- PLK4 p.Arg247His Uncertain significance ★★ ⚠ same type
- PLK4 p.Arg28Ser 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/plk4-p-pro679 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown