PDSS1 p.Val141=
c.423G>A · rs1835360004 · VCV2701988
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
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 6.5 | GERP 0.84, phastCons 1 |
| Overall | ||
| CADD | 11.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,914 alleles
Overall
6.2e-05%
1/1,613,832 alleles · very rare
exomes 0/1,461,682 · genomes 1/152,150 · 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.Val141=
- Coding
- c.423G>A
- MANE Select
- NM_014317
- dbSNP
- rs1835360004
- Type
- single nucleotide variant
- Location
- chr10:26709724 (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-val141 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown