KAT6B p.Ser1041=
c.3123G>A · VCV3611142
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0822%, mid)
Conditions
1
genitopatellar syndrome
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 0.23 | GERP -2.1, phastCons 0.85 |
| Overall | ||
| CADD | 9.308 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0822%
Middle Eastern · 5/6,084 alleles
Filtering AF
0.0323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.021%
Overall
0.000682%
11/1,613,990 alleles · ultra-rare
exomes 9/1,461,878 · genomes 2/152,112 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0822% | 1,217 |
| Finnishnot grpmax-eligible | 0.00156% | 64,014 |
| European (non-Finnish) | 0.000424% | 236,006 |
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
- KAT6B
- Protein
- p.Ser1041=
- Coding
- c.3123G>A
- MANE Select
- NM_012330
- Type
- single nucleotide variant
- Location
- chr10:75021982 (GRCh38)
- Gene constraint
- LOEUF 0.098 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.67 · 3 PDB
- Residue 1041
- the 'disordered' region
Similar variants
- KAT6B p.Ser1041Leu Benign/Likely benign ★★ same residue
- KAT6B p.Ser1041Ter Pathogenic ★ same residue
- KAT6B c.3664+1G>A Pathogenic ★★ same condition
- KAT6B p.Arg1058Ter Pathogenic ★★ same condition
- KAT6B p.Arg1797Ter Pathogenic ★★ same condition
- KAT6B p.Gln1752Ter Pathogenic ★★ same condition
- KAT6B c.2373+6C>A Uncertain significance ★★ same condition
- KAT6B c.2374-3T>C Uncertain significance ★★ same condition
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/kat6b-p-ser1041 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown