PRDM6 p.Ser465=
c.1395G>A · VCV4971779
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0171%, eas)
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 -5.8 | GERP -2.1 |
| Overall | ||
| CADD | 6.056 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0171%
East Asian · 7/40,908 alleles
Filtering AF
0.00819%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00639%
Overall
0.00535%
83/1,551,850 alleles · ultra-rare
exomes 77/1,399,588 · genomes 6/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0171% | 5,844 |
| South Asian | 0.0143% | 7,005 |
| African / African-American | 0.00547% | 18,288 |
| European (non-Finnish) | 0.00506% | 19,777 |
| Remaining individualsnot grpmax-eligible | 0.00332% | 30,077 |
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
- PRDM6
- Protein
- p.Ser465=
- Coding
- c.1395G>A
- MANE Select
- NM_001136239
- Type
- single nucleotide variant
- Location
- chr5:123171007 (GRCh38)
- Gene constraint
- LOEUF 0.649 · pLI 0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 57.72
Similar variants
- PRDM6 p.Leu26Phe Uncertain significance ★★ ⚠ same type
- PRDM6 p.Lys149Met Uncertain significance ★★ ⚠ same type
- PRDM6 p.Ser78Cys Uncertain significance ★★ ⚠ same type
- PRDM6 p.Cys503= Likely benign ★★ same type
- PRDM6 p.Gly153= Likely benign ★★ same type
- PRDM6 p.Pro56= Likely benign ★★ same type
- PRDM6 p.Ala101Pro Uncertain significance ★ ⚠ same type
- PRDM6 p.Ala102Pro 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/prdm6-p-ser465 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown