PDSS1 p.Val40=
c.120C>T · rs1427971854 · VCV1914323
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000578%, nfe)
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 · C>A here scores Δ0.56 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.32 | GERP -2.2 |
| Overall | ||
| CADD | 5.836 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000578%
European (non-Finnish) · 6/1,038,836 alleles
Filtering AF
0.000208%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000448%
6/1,339,012 alleles · very rare
exomes 6/1,186,860 · genomes 0/152,152 · joint denominator
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.Val40=
- Coding
- c.120C>T
- MANE Select
- NM_014317
- dbSNP
- rs1427971854
- Type
- single nucleotide variant
- Location
- chr10:26697831 (GRCh38)
- Gene constraint
- LOEUF 1.163 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.45
Similar variants
- 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
- PDSS1 p.Arg163Cys 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-val40 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown