PDSS1 p.Arg47=
c.139C>A · rs756296695 · VCV1956105
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 455,152)
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 -4.4 | GERP -0.26, phastCons 0.15 |
| Overall | ||
| CADD | 0.303 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 455,152). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- PDSS1
- Protein
- p.Arg47=
- Coding
- c.139C>A
- MANE Select
- NM_014317
- dbSNP
- rs756296695
- Type
- single nucleotide variant
- Location
- chr10:26702171 (GRCh38)
- Gene constraint
- LOEUF 1.163 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.45
Similar variants
- PDSS1 p.Arg47Gln Uncertain significance ★★ ⚠ same residue
- PDSS1 p.Arg47Trp 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
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-arg47 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown