PRDM13 p.Pro427=
c.1281G>A · rs138903323 · VCV768104
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.77%, 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 -10 | GERP -3.1 |
| Overall | ||
| CADD | 0.638 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.77%
African / African-American · 1,271/71,614 alleles
Filtering AF
1.69%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.66%
Overall
0.0869%
1,377/1,584,952 alleles · low-frequency
exomes 633/1,432,636 · genomes 744/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.77% | 56 |
| Remaining individualsnot grpmax-eligible | 0.0997% | 1,003 |
| Admixed American | 0.0569% | 1,757 |
| Middle Eastern | 0.0339% | 2,952 |
| South Asian | 0.00113% | 88,478 |
| European (non-Finnish) | 0.000854% | 117,070 |
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.Pro427=
- Coding
- c.1281G>A
- MANE Select
- NM_021620
- dbSNP
- rs138903323
- Type
- single nucleotide variant
- Location
- chr6:99613916 (GRCh38)
- Gene constraint
- LOEUF 0.694 · pLI 0.08 (gnomAD)
- Structure
- AlphaFold pLDDT 53.52
Similar variants
- PRDM13 p.Pro427Leu Uncertain significance ★ ⚠ same residue
- PRDM13 p.Pro427Ser Uncertain significance ★ ⚠ 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
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-pro427 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown