PRDM5 p.Cys522=
c.1566T>C · rs1365380507 · VCV1775390
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00268%, afr)
Conditions
1
Cardiovascular phenotype
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 0.82 | GERP -2.9, phastCons 0.97 |
| Overall | ||
| CADD | 7.214 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00268%
African / African-American · 2/74,618 alleles
Filtering AF
0.000445%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000167%
Overall
0.000187%
3/1,601,628 alleles · very rare
exomes 1/1,449,468 · genomes 2/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00268% | 37,309 |
| European (non-Finnish) | 8.55e-05% | 1,169,031 |
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.Cys522=
- Coding
- c.1566T>C
- MANE Select
- NM_018699
- dbSNP
- rs1365380507
- Type
- single nucleotide variant
- Location
- chr4:120754610 (GRCh38)
- Gene constraint
- LOEUF 0.899 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.53 · 1 PDB
Similar variants
- PRDM5 p.Cys522Tyr Uncertain significance ★ ⚠ same residue
- PRDM5 p.Gln556Ter Pathogenic/Likely pathogenic ★★ same condition
- PRDM5 c.650+5G>A Uncertain significance ★★ same condition
- PRDM5 c.744-3T>C Uncertain significance ★★ same condition
- PRDM5 p.Ala155Val Uncertain significance ★★ ⚠ same condition
- PRDM5 p.Ala469Val Uncertain significance ★★ same condition
- PRDM5 p.Arg257Pro Uncertain significance ★★ ⚠ same condition
- PRDM5 p.Arg257Trp Uncertain significance ★★ ⚠ same condition
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-cys522 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown