NDST1 p.Phe322=
c.966C>T · rs11959543 · VCV715605
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.75%, afr)
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 -6 | GERP -5.6 |
| Overall | ||
| CADD | 1.731 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.75%
African / African-American · 1,311/74,970 alleles
Filtering AF
1.67%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.64%
Overall
0.093%
1,496/1,608,642 alleles · low-frequency
exomes 714/1,456,322 · genomes 782/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.75% | 57 |
| Admixed American | 0.142% | 705 |
| Remaining individualsnot grpmax-eligible | 0.0996% | 1,004 |
| Middle Eastern | 0.0662% | 1,511 |
| South Asian | 0.0099% | 10,100 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00677% | 14,765 |
| European (non-Finnish) | 0.00196% | 51,106 |
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.Phe322=
- Coding
- c.966C>T
- MANE Select
- NM_001543
- dbSNP
- rs11959543
- Type
- single nucleotide variant
- Location
- chr5:150528256 (GRCh38)
- Gene constraint
- LOEUF 0.484 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 90.55 · 5 PDB
- Residue 322
- the 'heparan sulfate n-deacetylase 1' region
Similar variants
- 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
- NDST1 p.Arg454Cys 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-phe322 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown