SETD1A p.Pro654=
c.1962G>A · VCV3905307
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0248%, 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 -1.1 | GERP -4.4, phastCons 0.001 |
| Overall | ||
| CADD | 4.643 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0248%
Middle Eastern · 1/4,030 alleles
Filtering AF
0.000986%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00076%
Overall
0.0017%
17/999,664 alleles · ultra-rare
exomes 16/922,916 · genomes 1/76,748 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0248% | 4,030 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00631% | 15,856 |
| East Asian | 0.00544% | 18,384 |
| Remaining individualsnot grpmax-eligible | 0.00284% | 35,150 |
| European (non-Finnish) | 0.00177% | 56,552 |
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
- SETD1A
- Protein
- p.Pro654=
- Coding
- c.1962G>A
- MANE Select
- NM_014712
- Type
- single nucleotide variant
- Location
- chr16:30965843 (GRCh38)
- Gene constraint
- LOEUF 0.279 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.20 · 4 PDB
- Residue 654
- a UniProt-annotated variant site (in nedsid); the 'disordered' region
Similar variants
- SETD1A p.Pro654fs Likely pathogenic ★ same residue
- SETD1A p.Pro654del Uncertain significance ★ same residue
- SETD1A c.518-2A>G Pathogenic ★★ same type
- SETD1A p.Arg1571Ter Pathogenic/Likely pathogenic ★★ same type
- SETD1A p.Arg176Ter Pathogenic/Likely pathogenic ★★ same type
- SETD1A p.Arg668Ter Pathogenic ★★ same type
- SETD1A p.Arg913Cys Likely pathogenic ★★ ⚠ same type
- SETD1A p.Arg990Ter 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/setd1a-p-pro654 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown