PPID p.Asp359=
c.1077T>C · VCV3341521
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.29%, mid)
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 0.76 | GERP -4.7, phastCons 0.98 |
| Overall | ||
| CADD | 6.519 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.29%
Middle Eastern · 78/6,048 alleles
Filtering AF
1.06%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.974%
Overall
0.247%
3,977/1,611,976 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.29% | 78 |
| South Asian | 0.433% | 231 |
| Ashkenazi Jewishnot grpmax-eligible | 0.375% | 267 |
| Remaining individualsnot grpmax-eligible | 0.317% | 315 |
| European (non-Finnish) | 0.257% | 389 |
| Admixed American | 0.172% | 582 |
| Finnishnot grpmax-eligible | 0.0427% | 2,339 |
| African / African-American | 0.0413% | 2,421 |
| East Asian | 0.00446% | 22,411 |
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
- PPID
- Protein
- p.Asp359=
- Coding
- c.1077T>C
- MANE Select
- NM_005038
- Type
- single nucleotide variant
- Location
- chr4:158709772 (GRCh38)
- Gene constraint
- LOEUF 1.303 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.51
- Residue 359
- the 'interaction with hsp90ab1' region
Similar variants
- PPID p.Val177Ile Benign ★★ same type
- PPID p.Ala299Pro Uncertain significance ★ ⚠ same type
- PPID p.Ala326Thr Uncertain significance ★ ⚠ same type
- PPID p.Ala356Thr Uncertain significance ★ ⚠ same type
- PPID p.Arg125His Uncertain significance ★ ⚠ same type
- PPID p.Arg312Cys Uncertain significance ★ ⚠ same type
- PPID p.Arg312His Uncertain significance ★ same type
- PPID p.Arg31Gln 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/ppid-p-asp359 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown