PDSS2 p.Thr152=
c.456G>A · rs374369326 · VCV1293080
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.005%, nfe)
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 0.1 | GERP -4, phastCons 0.99 |
| Overall | ||
| CADD | 9.338 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
European (non-Finnish) · 59/1,179,638 alleles
Filtering AF
0.00394%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00361%
Overall
0.0039%
63/1,613,568 alleles · very rare
exomes 60/1,461,438 · genomes 3/152,130 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.005% | 19,994 |
| African / African-American | 0.00401% | 24,962 |
| East Asian | 0.00223% | 44,894 |
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
- PDSS2
- Protein
- p.Thr152=
- Coding
- c.456G>A
- MANE Select
- NM_020381
- dbSNP
- rs374369326
- Type
- single nucleotide variant
- Location
- chr6:107274203 (GRCh38)
- Gene constraint
- LOEUF 0.818 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.28
Similar variants
- PDSS2 p.Thr152Met Uncertain significance ★ ⚠ same residue
- PDSS2 p.Arg163His Uncertain significance ★★ ⚠ same type
- PDSS2 p.Arg366Cys Uncertain significance ★★ ⚠ same type
- PDSS2 p.Arg366His Uncertain significance ★★ ⚠ same type
- PDSS2 p.Arg385Thr Uncertain significance ★★ ⚠ same type
- PDSS2 p.Asn167Ser Uncertain significance ★★ ⚠ same type
- PDSS2 p.Asn201Ser Uncertain significance ★★ ⚠ same type
- PDSS2 p.Asn314Thr 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/pdss2-p-thr152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown