NDP p.Ser80=
c.240G>A · VCV4691217
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00712%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -3.7, phastCons 1 |
| Overall | ||
| CADD | 12.82 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00712%
South Asian · 4/56,148 alleles
Filtering AF
0.00236%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00142%
Overall
0.000745%
9/1,208,741 alleles · very rare
exomes 9/1,095,129 · genomes 0/113,612 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00712% | 14,037 |
| European (non-Finnish) | 0.000559% | 178,834 |
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.Ser80=
- Coding
- c.240G>A
- MANE Select
- NM_000266
- Type
- single nucleotide variant
- Location
- chrX:43949961 (GRCh38)
- Structure
- AlphaFold pLDDT 83.92 · 12 PDB
- Residue 80
- the ctck domain; a β-strand
Similar variants
- NDP p.Ser80Leu Uncertain significance ⚠ same residue
- 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
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-ser80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown