NDST1 p.Pro16=
c.48G>A · rs139789204 · VCV721689
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.184%, sas)
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 -7.8 | GERP -3.5 |
| Overall | ||
| CADD | 7.062 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.184%
South Asian · 168/91,080 alleles
Filtering AF
0.162%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.153%
Overall
0.0138%
223/1,612,804 alleles · rare
exomes 187/1,460,548 · genomes 36/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.184% | 542 |
| African / African-American | 0.04% | 2,502 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,416 |
| East Asian | 0.00892% | 11,207 |
| Admixed American | 0.005% | 20,009 |
| European (non-Finnish) | 0.00102% | 98,325 |
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
- NDST1
- Protein
- p.Pro16=
- Coding
- c.48G>A
- MANE Select
- NM_001543
- dbSNP
- rs139789204
- Type
- single nucleotide variant
- Location
- chr5:150521302 (GRCh38)
- Gene constraint
- LOEUF 0.484 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 90.55 · 5 PDB
- Residue 16
- the 'sufficient for localization to golgi membrane' region
Similar variants
- NDST1 p.Pro16Leu Uncertain significance ★ ⚠ same residue
- NDST1 p.Gly611Ser Pathogenic/Likely pathogenic ★★ same type
- NDST1 c.1008+4T>A Uncertain significance ★★ same type
- NDST1 p.Ala256Thr Uncertain significance ★★ ⚠ same type
- NDST1 p.Ala697Val Uncertain significance ★★ ⚠ same type
- NDST1 p.Arg112Cys Uncertain significance ★★ ⚠ same type
- NDST1 p.Arg130Cys Uncertain significance ★★ ⚠ same type
- NDST1 p.Arg244Cys 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/ndst1-p-pro16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown