PRDM13 p.Pro441=
c.1323G>A · rs769989460 · VCV1472458
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0125%, 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 -1.7 | GERP -3.1 |
| Overall | ||
| CADD | 1.105 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0125%
African / African-American · 9/72,088 alleles
Filtering AF
0.00645%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00483%
Overall
0.000816%
13/1,593,188 alleles · ultra-rare
exomes 8/1,440,988 · genomes 5/152,200 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0125% | 8,010 |
| Remaining individualsnot grpmax-eligible | 0.00325% | 30,778 |
| Admixed American | 0.00174% | 57,454 |
| European (non-Finnish) | 8.52e-05% | 1,173,215 |
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.Pro441=
- Coding
- c.1323G>A
- MANE Select
- NM_021620
- dbSNP
- rs769989460
- Type
- single nucleotide variant
- Location
- chr6:99613958 (GRCh38)
- Gene constraint
- LOEUF 0.694 · pLI 0.08 (gnomAD)
- Structure
- AlphaFold pLDDT 53.52
Similar variants
- 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
- PRDM13 p.Ala5Ser 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-pro441 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown