PRDM13 p.Ala552=
c.1656G>T · rs1021739985 · VCV1136182
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0254%, afr)
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 -0.47 | GERP -3.7, phastCons 0.006 |
| Overall | ||
| CADD | 5.501 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0254%
African / African-American · 19/74,740 alleles
Filtering AF
0.0166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0138%
Overall
0.00149%
24/1,605,618 alleles · ultra-rare
exomes 13/1,453,426 · genomes 11/152,192 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0254% | 3,934 |
| Remaining individualsnot grpmax-eligible | 0.00484% | 20,668 |
| Admixed American | 0.00169% | 59,292 |
| South Asian | 0.0011% | 90,556 |
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
- PRDM13
- Protein
- p.Ala552=
- Coding
- c.1656G>T
- MANE Select
- NM_021620
- dbSNP
- rs1021739985
- Type
- single nucleotide variant
- Location
- chr6:99614291 (GRCh38)
- Gene constraint
- LOEUF 0.694 · pLI 0.08 (gnomAD)
- Structure
- AlphaFold pLDDT 53.52
- Residue 552
- the 'disordered' region
Similar variants
- PRDM13 p.Ala552Val Benign/Likely benign ★★ same residue
- PRDM13 c.277-10T>G Uncertain significance ★★ same type
- PRDM13 p.Ala231Val Uncertain significance ★★ ⚠ same type
- PRDM13 p.Ala258Val Uncertain significance ★★ ⚠ same type
- PRDM13 p.Ala298Pro Uncertain significance ★★ ⚠ same type
- PRDM13 p.Ala414Glu Uncertain significance ★★ ⚠ same type
- PRDM13 p.Ala510Thr Uncertain significance ★★ ⚠ same type
- PRDM13 p.Ala566Thr 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/prdm13-p-ala552 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown