PRDM5 p.Ala26=
c.78C>T · rs2479842456 · VCV2748013
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 4.4 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 14.84 | PHRED · no single calibrated threshold — expert panels disagree |
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
- PRDM5
- Protein
- p.Ala26=
- Coding
- c.78C>T
- MANE Select
- NM_018699
- dbSNP
- rs2479842456
- Type
- single nucleotide variant
- Location
- chr4:120922531 (GRCh38)
- Gene constraint
- LOEUF 0.899 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.53 · 1 PDB
- Residue 26
- the set domain; a β-strand
Similar variants
- PRDM5 p.Ala26Thr Uncertain significance ★ ⚠ same residue
- PRDM5 c.1623+1G>A Likely pathogenic ★★ same type
- PRDM5 c.865+1G>A Likely pathogenic ★★ same type
- PRDM5 p.Arg232Ter Pathogenic/Likely pathogenic ★★ same type
- PRDM5 p.Arg346Ter Pathogenic ★★ same type
- PRDM5 p.Gln420Ter Pathogenic/Likely pathogenic ★★ same type
- PRDM5 p.Gln556Ter Pathogenic/Likely pathogenic ★★ same type
- PRDM5 p.Glu103Ter Pathogenic/Likely pathogenic ★★ 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/prdm5-p-ala26 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown