PDSS1 p.Pro26=
c.78C>G · rs1039558873 · VCV1941424
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0113%, sas)
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 -20 | GERP -2.6 |
| Overall | ||
| CADD | 0.083 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0113%
South Asian · 5/44,360 alleles
Filtering AF
0.00439%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00279%
Overall
0.00244%
32/1,309,786 alleles · ultra-rare
exomes 27/1,157,706 · genomes 5/152,080 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0113% | 8,872 |
| European (non-Finnish) | 0.00261% | 38,253 |
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
- PDSS1
- Protein
- p.Pro26=
- Coding
- c.78C>G
- MANE Select
- NM_014317
- dbSNP
- rs1039558873
- Type
- single nucleotide variant
- Location
- chr10:26697789 (GRCh38)
- Gene constraint
- LOEUF 1.163 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.45
- Residue 26
- the 'disordered' region
Similar variants
- PDSS1 p.Pro26Leu Uncertain significance ★ ⚠ same residue
- PDSS1 p.Arg221Ter Likely pathogenic ★★ same type
- PDSS1 p.Trp6Ter Likely pathogenic ★★ same type
- PDSS1 c.129+5G>C Uncertain significance ★★ same type
- PDSS1 c.721+4C>T Uncertain significance ★★ same type
- PDSS1 p.Ala268Thr Uncertain significance ★★ ⚠ same type
- PDSS1 p.Ala380Thr Uncertain significance ★★ ⚠ same type
- PDSS1 p.Arg146Gln 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/pdss1-p-pro26 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown