NDST1 p.Pro706=
c.2118C>T · rs145787796 · VCV720304
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00991%, nfe)
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 -8 | GERP -5.7 |
| Overall | ||
| CADD | 2.537 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00991%
European (non-Finnish) · 117/1,180,050 alleles
Filtering AF
0.00842%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00787%
Overall
0.00774%
125/1,614,138 alleles · very rare
exomes 119/1,461,876 · genomes 6/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00991% | 10,086 |
| East Asian | 0.00445% | 22,453 |
| African / African-American | 0.004% | 24,984 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| South Asian | 0.0011% | 91,092 |
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.Pro706=
- Coding
- c.2118C>T
- MANE Select
- NM_001543
- dbSNP
- rs145787796
- Type
- single nucleotide variant
- Location
- chr5:150545459 (GRCh38)
- Gene constraint
- LOEUF 0.484 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 90.55 · 5 PDB
- Residue 706
- the 'heparan sulfate n-sulfotransferase 1' region; an α-helix
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-pro706 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown