KAT6B p.Val997=
c.2991G>A · rs1421489322 · VCV1160721
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000424%, nfe)
Conditions
2
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 3 | GERP 0.69, phastCons 1 |
| Overall | ||
| CADD | 5.463 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000424%
European (non-Finnish) · 5/1,180,030 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.00031%
5/1,614,182 alleles · very rare
exomes 5/1,461,864 · genomes 0/152,318 · 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
- KAT6B
- Protein
- p.Val997=
- Coding
- c.2991G>A
- MANE Select
- NM_012330
- dbSNP
- rs1421489322
- Type
- single nucleotide variant
- Location
- chr10:75021255 (GRCh38)
- Gene constraint
- LOEUF 0.098 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.67 · 3 PDB
- Residue 997
- the 'catalytic' region; the 'interaction with brpf1' region
Similar variants
- KAT6B c.3664+1G>A Pathogenic ★★ same condition
- KAT6B p.Arg1058Ter Pathogenic ★★ same condition
- KAT6B p.Arg1797Ter Pathogenic ★★ same condition
- KAT6B p.Arg783Ter Pathogenic/Likely pathogenic ★★ same condition
- KAT6B p.Gln1014Ter Pathogenic ★★ same condition
- KAT6B p.Gln1752Ter Pathogenic ★★ same condition
- KAT6B p.Gln1768Ter Pathogenic ★★ same condition
- KAT6B p.Glu1073Ter Pathogenic ★★ 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-val997 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown