SETD1B p.Ser580=
c.1740C>T · VCV4871919
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, mid)
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 -9.6 | GERP -3.5 |
| Overall | ||
| CADD | 0.031 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Middle Eastern · 1/5,990 alleles
Filtering AF
0.00354%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00243%
Overall
0.00103%
16/1,550,666 alleles · ultra-rare
exomes 11/1,398,326 · genomes 5/152,340 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0167% | 5,990 |
| African / African-American | 0.0082% | 12,195 |
| East Asian | 0.00244% | 40,916 |
| Admixed American | 0.00196% | 50,994 |
| South Asian | 0.00119% | 84,026 |
| European (non-Finnish) | 0.000523% | 191,150 |
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
- SETD1B
- Protein
- p.Ser580=
- Coding
- c.1740C>T
- MANE Select
- NM_001353345
- Type
- single nucleotide variant
- Location
- chr12:121810685 (GRCh38)
- Gene constraint
- LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 46.43 · 4 PDB
- Residue 580
- the 'disordered' region
Similar variants
- SETD1B p.Ser580Pro Uncertain significance ★ ⚠ same residue
- SETD1B p.Arg1329Ter Pathogenic ★★ same type
- SETD1B p.Arg1703Ter Pathogenic/Likely pathogenic ★★ same type
- SETD1B p.Arg1748Cys Pathogenic/Likely pathogenic ★★ same type
- SETD1B p.Arg1792Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- SETD1B p.Arg1825Trp Likely pathogenic ★★ same type
- SETD1B p.Arg1902Cys Pathogenic/Likely pathogenic ★★ same type
- SETD1B p.Gln780Ter Pathogenic/Likely pathogenic ★★ 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/setd1b-p-ser580 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown