NDST1 p.Ser48=
c.144G>A · rs144715747 · VCV435942
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.324%, 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 -12 | GERP -3.8 |
| Overall | ||
| CADD | 0.252 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.324%
African / African-American · 243/75,012 alleles
Filtering AF
0.291%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.278%
Overall
0.0184%
297/1,613,198 alleles · rare
exomes 156/1,460,994 · genomes 141/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.324% | 309 |
| Admixed American | 0.0183% | 5,457 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,812 |
| South Asian | 0.00878% | 11,386 |
| European (non-Finnish) | 0.0022% | 45,380 |
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.Ser48=
- Coding
- c.144G>A
- MANE Select
- NM_001543
- dbSNP
- rs144715747
- Type
- single nucleotide variant
- Location
- chr5:150521398 (GRCh38)
- Gene constraint
- LOEUF 0.484 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 90.55 · 5 PDB
- Residue 48
- the 'sufficient for localization to golgi membrane' region; the 'heparan sulfate n-deacetylase 1' region
Similar variants
- NDST1 p.Ser48Pro Uncertain significance ★ ⚠ same residue
- NDST1 p.Ser48Trp Uncertain significance ★ ⚠ same residue
- NDST1 p.Ser48fs 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
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-ser48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown