PTDSS1 p.Ser320=
c.960T>C · rs758177724 · VCV1962701
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.034%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>G here scores Δ0.37 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -3.7, phastCons 0.002 |
| Overall | ||
| CADD | 5.731 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.034%
South Asian · 31/91,084 alleles
Filtering AF
0.0246%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0214%
Overall
0.00198%
32/1,614,008 alleles · ultra-rare
exomes 30/1,461,816 · genomes 2/152,192 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.034% | 2,938 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,486 |
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
- PTDSS1
- Protein
- p.Ser320=
- Coding
- c.960T>C
- MANE Select
- NM_014754
- dbSNP
- rs758177724
- Type
- single nucleotide variant
- Location
- chr8:96306509 (GRCh38)
- Gene constraint
- LOEUF 0.776 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.33 · 6 PDB
- Residue 320
- an α-helix
Similar variants
- PTDSS1 p.Arg95Gln Pathogenic/Likely pathogenic ★★ same type
- PTDSS1 p.Ala140Thr Uncertain significance ★★ ⚠ same type
- PTDSS1 p.Arg238Gln Uncertain significance ★★ ⚠ same type
- PTDSS1 p.Glu212Lys Uncertain significance ★★ ⚠ same type
- PTDSS1 p.Gly229Asp Uncertain significance ★★ ⚠ same type
- PTDSS1 p.His246Gln Uncertain significance ★★ ⚠ same type
- PTDSS1 p.Leu292Phe Uncertain significance ★★ ⚠ same type
- PTDSS1 p.Leu307Trp 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/ptdss1-p-ser320 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown