SETD1B p.Ser1929=
c.5787G>A · VCV4919051
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0793%, 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 -7.9 | GERP -4.2 |
| Overall | ||
| CADD | 0.632 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0793%
African / African-American · 58/73,132 alleles
Filtering AF
0.0629%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.057%
Overall
0.00761%
118/1,551,488 alleles · ultra-rare
exomes 80/1,399,238 · genomes 38/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0793% | 1,261 |
| Middle Eastern | 0.0502% | 1,993 |
| Remaining individualsnot grpmax-eligible | 0.0283% | 3,535 |
| South Asian | 0.019% | 5,254 |
| Admixed American | 0.0118% | 8,499 |
| East Asian | 0.00489% | 20,451 |
| Finnishnot grpmax-eligible | 0.00334% | 29,952 |
| European (non-Finnish) | 0.00122% | 81,919 |
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.Ser1929=
- Coding
- c.5787G>A
- MANE Select
- NM_001353345
- Type
- single nucleotide variant
- Location
- chr12:121830125 (GRCh38)
- Gene constraint
- LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 46.43 · 4 PDB
- Residue 1929
- the set domain; a UniProt-annotated variant site (in iddseld)
Similar variants
- 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
- SETD1B p.Glu1948Lys 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-ser1929 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown