NEK2 p.Pro237=
c.711A>G · rs763334603 · VCV2746932
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00669%, 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 -7 | GERP -4.1 |
| Overall | ||
| CADD | 2.449 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00669%
East Asian · 3/44,876 alleles
Filtering AF
0.00286%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00195%
Overall
0.00155%
25/1,613,140 alleles · very rare
exomes 21/1,460,914 · genomes 4/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00669% | 14,959 |
| South Asian | 0.00659% | 15,173 |
| African / African-American | 0.00267% | 37,456 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,454 |
| European (non-Finnish) | 0.0011% | 90,715 |
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
- NEK2
- Protein
- p.Pro237=
- Coding
- c.711A>G
- MANE Select
- NM_002497
- dbSNP
- rs763334603
- Type
- single nucleotide variant
- Location
- chr1:211670335 (GRCh38)
- Gene constraint
- LOEUF 0.648 · pLI 0.04 (gnomAD)
- Structure
- AlphaFold pLDDT 78.52 · 30 PDB
- Residue 237
- the protein kinase domain; an α-helix
Similar variants
- NEK2 c.97-2A>G Uncertain significance ★★ same type
- NEK2 p.Arg130Gln Uncertain significance ★★ same type
- NEK2 p.Arg130Gly Uncertain significance ★★ ⚠ same type
- NEK2 p.Arg140Gln Uncertain significance ★★ ⚠ same type
- NEK2 p.Arg239His Uncertain significance ★★ ⚠ same type
- NEK2 p.Arg239Ser Uncertain significance ★★ ⚠ same type
- NEK2 p.Arg318Gln Uncertain significance ★★ ⚠ same type
- NEK2 p.Arg318Ter 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/nek2-p-pro237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown