NEK8 p.Ser151=
c.453C>T · rs2034348487 · VCV1712435
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
1
kidney disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.26 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.83 | GERP -0.72, phastCons 1 |
| Overall | ||
| CADD | 13.76 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,976 alleles
Overall
6.2e-05%
1/1,613,176 alleles · very rare
exomes 1/1,460,970 · genomes 0/152,206 · joint denominator
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
- NEK8
- Protein
- p.Ser151=
- Coding
- c.453C>T
- MANE Select
- NM_178170
- dbSNP
- rs2034348487
- Type
- single nucleotide variant
- Location
- chr17:28734971 (GRCh38)
- Gene constraint
- LOEUF 0.835 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.23
- Residue 151
- the protein kinase domain; a UniProt-annotated variant site (in rhpd2; likely pathogenic; loss of protein expression)
Similar variants
- NEK8 p.Met413Leu Conflicting classifications of pathogenicity ★ ⚠ same condition
- NEK8 c.1732+8_1732+10del Benign/Likely benign ★★ same condition
- NEK8 c.1418-1G>A Pathogenic/Likely pathogenic ★★ same type
- NEK8 c.828-1G>C Pathogenic/Likely pathogenic ★★ same type
- NEK8 c.889+1G>T Likely pathogenic ★★ same type
- NEK8 p.Arg127Ter Pathogenic/Likely pathogenic ★★ same type
- NEK8 p.Arg499Ter Pathogenic/Likely pathogenic ★★ same type
- NEK8 p.Arg599Ter Pathogenic/Likely pathogenic ★★ 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/nek8-p-ser151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown