NDE1 p.Asp171=
c.513T>C · rs794727785 · VCV198124
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
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 0.5 | GERP -0.76, phastCons 1 |
| Overall | ||
| CADD | 8.066 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,082 alleles
Filtering AF
0.0058%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00241%
Overall
0.000744%
12/1,613,958 alleles · ultra-rare
exomes 10/1,461,738 · genomes 2/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,041 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| Admixed American | 0.00167% | 60,006 |
| European (non-Finnish) | 0.000508% | 196,667 |
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.Asp171=
- Coding
- c.513T>C
- MANE Select
- NM_017668
- dbSNP
- rs794727785
- Type
- single nucleotide variant
- Location
- chr16:15687501 (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 171
- the 'interaction with cenpf' 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-asp171 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown