NDE1 p.Ser309=
c.927C>T · VCV4928643
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.2 | GERP -4.3 |
| Overall | ||
| CADD | 1.263 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,858 alleles
Filtering AF
0.000615%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000474%
Overall
0.000867%
14/1,614,140 alleles · very rare
exomes 14/1,461,866 · genomes 0/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,858 |
| European (non-Finnish) | 0.0011% | 90,770 |
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
- NDE1
- Protein
- p.Ser309=
- Coding
- c.927C>T
- MANE Select
- NM_017668
- Type
- single nucleotide variant
- Location
- chr16:15696840 (GRCh38)
- Gene constraint
- LOEUF 0.851 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.40 · 1 PDB
- Residue 309
- a modified residue (phosphoserine); the 'disordered' region
Similar variants
- NDE1 p.Arg220Ter Pathogenic/Likely pathogenic ★★ same type
- NDE1 p.Arg37Ter Pathogenic ★★ same type
- MYH11 c.4578+6T>C Uncertain significance ★★ same type
- MYH11 c.4791+5G>A Uncertain significance ★★ same type
- MYH11 c.4954-3C>G Uncertain significance ★★ same type
- MYH11 c.5787-4685C>T Uncertain significance ★★ same type
- MYH11 p.Ala1311Glu Uncertain significance ★★ ⚠ same type
- MYH11 p.Ala1311Thr 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/nde1-p-ser309 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown