NDE1 p.Asp237=
c.711C>T · rs148344039 · VCV382222
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.367%, 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 -8.4 | GERP -4.1 |
| Overall | ||
| CADD | 2.133 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.367%
Middle Eastern · 18/4,904 alleles
Filtering AF
0.237%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.196%
Overall
0.00477%
77/1,612,604 alleles · rare
exomes 66/1,460,356 · genomes 11/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.367% | 272 |
| African / African-American | 0.024% | 4,165 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,796 |
| Finnishnot grpmax-eligible | 0.00781% | 12,799 |
| European (non-Finnish) | 0.0022% | 45,384 |
| Admixed American | 0.00167% | 60,008 |
| South Asian | 0.0011% | 90,990 |
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.Asp237=
- Coding
- c.711C>T
- MANE Select
- NM_017668
- dbSNP
- rs148344039
- Type
- single nucleotide variant
- Location
- chr16:15694172 (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 237
- the 'interaction with cenpf' region; 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-asp237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown