PTDSS1 p.Pro92=
c.276G>A · rs762184286 · VCV1981533
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00893%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.9 | GERP -3.4 |
| Overall | ||
| CADD | 3.509 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00893%
East Asian · 4/44,806 alleles
Filtering AF
0.00521%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00475%
Overall
0.00522%
84/1,608,592 alleles · very rare
exomes 83/1,456,522 · genomes 1/152,070 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00893% | 11,201 |
| European (non-Finnish) | 0.00638% | 15,680 |
| South Asian | 0.00442% | 22,637 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,324 |
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.Pro92=
- Coding
- c.276G>A
- MANE Select
- NM_014754
- dbSNP
- rs762184286
- Type
- single nucleotide variant
- Location
- chr8:96284113 (GRCh38)
- Gene constraint
- LOEUF 0.776 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.33 · 6 PDB
Similar variants
- PTDSS1 p.Pro92Leu Uncertain significance ★★ ⚠ same residue
- 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
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-pro92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown