NDE1 p.Phe39=
c.117C>T · rs797045732 · VCV211576
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 1.4 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 13.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- NDE1
- Protein
- p.Phe39=
- Coding
- c.117C>T
- MANE Select
- NM_017668
- dbSNP
- rs797045732
- Type
- single nucleotide variant
- Location
- chr16:15667319 (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 39
- the 'self-association' region
Similar variants
- NDE1 p.Phe39Ser Uncertain significance ★ ⚠ same residue
- 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
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-phe39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown