NDP p.Ser57=
c.171A>T · rs1569245603 · VCV1633631
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00296%, 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 0.41 | GERP 0.5, phastCons 1 |
| Overall | ||
| CADD | 9.853 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00296%
East Asian · 1/33,832 alleles
Filtering AF
0.00091%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000712%
Overall
0.00132%
16/1,208,488 alleles · very rare
exomes 16/1,094,444 · genomes 0/114,044 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00296% | 33,832 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,535 |
| European (non-Finnish) | 0.00157% | 63,730 |
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
- NDP
- Protein
- p.Ser57=
- Coding
- c.171A>T
- MANE Select
- NM_000266
- dbSNP
- rs1569245603
- Type
- single nucleotide variant
- Location
- chrX:43958475 (GRCh38)
- Structure
- AlphaFold pLDDT 83.92 · 12 PDB
- Residue 57
- the ctck domain
Similar variants
- NDP p.Ala118Asp Pathogenic/Likely pathogenic ★★ same type
- NDP p.Arg109Ter Pathogenic ★★ same type
- NDP p.Arg115Ter Pathogenic ★★ same type
- NDP p.Arg121Trp Pathogenic/Likely pathogenic ★★ same type
- NDP p.Arg37Ter Pathogenic/Likely pathogenic ★★ same type
- NDP p.Arg38Cys Pathogenic ★★ same type
- NDP p.Arg74Cys Pathogenic ★★ same type
- NDP p.Cys110Phe 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/ndp-p-ser57 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown