PRDM9 p.Asp324Glu
c.972T>A · VCV4144051
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.428 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| AlphaMissense | 0.428 | ambiguous |
|---|---|---|
| REVEL | 0.327 | indeterminate |
| SaProt | LLR -11.65 | damaging |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -15 | |
| Regional constraint | o/e 0.93 | unconstrained · MANE · 18 kb · p 0.061 · regional, not allelic |
| Overall | ||
| CADD | 16.84 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PRDM9
- Protein
- p.Asp324Glu
- Coding
- c.972T>A
- MANE Select
- NM_020227
- Type
- single nucleotide variant
- Location
- chr5:23524355 (GRCh38)
- Gene constraint
- LOEUF 1.039 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.19 · 5 PDB
- Residue 324
- the set domain
Similar variants
- PRDM9 c.301+67A>G Benign ★★ same type
- PRDM9 c.509-41C>T Benign ★★ same type
- PRDM9 c.883-52C>T Benign ★★ same type
- PRDM9 c.*125G>A Benign ★★ same type
- PRDM9 c.*37A>G Benign ★★ same type
- PRDM9 p.Asn790His Likely benign ★★ same type
- PRDM9 p.Asp30= Benign ★★ same type
- PRDM9 p.Gly144= Benign ★★ 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/prdm9-p-asp324glu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown