SETD1B p.Ala320=
c.960C>A · rs369474009 · VCV2643420
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000523%, 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 0.083 | GERP -2.1, phastCons 0.91 |
| Overall | ||
| CADD | 7.738 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000523%
European (non-Finnish) · 6/1,146,998 alleles
Filtering AF
0.000188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000124%
Overall
0.000387%
6/1,550,876 alleles · very rare
exomes 5/1,398,696 · genomes 1/152,180 · 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
- SETD1B
- Protein
- p.Ala320=
- Coding
- c.960C>A
- MANE Select
- NM_001353345
- dbSNP
- rs369474009
- Type
- single nucleotide variant
- Location
- chr12:121809905 (GRCh38)
- Gene constraint
- LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 46.43 · 4 PDB
Similar variants
- SETD1B p.Ala320Val Uncertain significance ★★ ⚠ same residue
- SETD1B p.Ala320Gly Uncertain significance ★ same residue
- SETD1B p.Ala320Thr Uncertain significance ★ same residue
- SETD1B p.Ala320fs Likely pathogenic ★ 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
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-ala320 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown