SETDB1 p.Thr320=
c.960T>C · rs769484858 · VCV741352
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00136%, nfe)
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 -7.9 | GERP -3.4 |
| Overall | ||
| CADD | 0.847 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00136%
European (non-Finnish) · 16/1,180,022 alleles
Filtering AF
0.000803%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00065%
Overall
0.000991%
16/1,613,952 alleles · very rare
exomes 14/1,461,854 · genomes 2/152,098 · joint denominator
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
- SETDB1
- Protein
- p.Thr320=
- Coding
- c.960T>C
- MANE Select
- NM_001366418
- dbSNP
- rs769484858
- Type
- single nucleotide variant
- Location
- chr1:150944928 (GRCh38)
- Gene constraint
- LOEUF 0.29 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.45 · 26 PDB
- Residue 320
- the tudor 2 domain; an α-helix
Similar variants
- SETDB1 c.261-3T>C Likely benign ★★ same type
- SETDB1 p.Ala1022Val Benign ★★ same type
- SETDB1 p.Pro469= Benign ★★ same type
- SETDB1 p.Pro530Leu Benign/Likely benign ★★ same type
- SETDB1 p.Pro978Leu Likely benign ★★ same type
- SETDB1 c.674-2A>G Uncertain significance ★ same type
- SETDB1 p.Arg1244Leu Uncertain significance ★ ⚠ same type
- SETDB1 p.Arg611Gln 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/setdb1-p-thr320 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown