PRDM5 p.Pro516=
c.1548C>T · rs573435327 · VCV740978
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
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 0.2 | GERP -0.93, phastCons 0.92 |
| Overall | ||
| CADD | 8.174 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/59,950 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000313%
5/1,596,760 alleles · very rare
exomes 4/1,444,648 · genomes 1/152,112 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 19,983 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 61,934 |
| African / African-American | 0.00134% | 74,486 |
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
- PRDM5
- Protein
- p.Pro516=
- Coding
- c.1548C>T
- MANE Select
- NM_018699
- dbSNP
- rs573435327
- Type
- single nucleotide variant
- Location
- chr4:120754628 (GRCh38)
- Gene constraint
- LOEUF 0.899 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.53 · 1 PDB
Similar variants
- 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
- PRDM5 p.Glu344Ter 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-pro516 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown