Is KAT6B p.Pro1809fs (c.5426del) pathogenic?

KAT6B p.Pro1809fs (c.5426del) is classified Likely pathogenic in KAT6B (ClinVar, Single submitter, 1 submitter). Associated with genitopatellar syndrome.

What condition is associated with KAT6B p.Pro1809fs (c.5426del)?

KAT6B p.Pro1809fs (c.5426del) is associated with genitopatellar syndrome, blepharophimosis - intellectual disability syndrome, SBBYS type (ClinVar).

KAT6B p.Pro1809fs

c.5426del · VCV3382234

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

genitopatellar syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon in the last exon (18 of 18) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.8, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: KAT6B
Protein: p.Pro1809fs
Coding: c.5426del
MANE Select: NM_012330
Type: Deletion
Location: chr10:75030248 (GRCh38)
Gene constraint: LOEUF 0.098 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 49.67 · 3 PDB
Residue 1809: the 'interaction with runx1 and runx2' region

Full KAT6B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

genitopatellar syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: blepharophimosis - intellectual disability syndrome, SBBYS type

Similar variants

KAT6B p.Pro1809Leu Uncertain significance ★★ ⚠ same residue
KAT6B p.Pro1809= Likely benign ★★ same residue
KAT6B p.Asn1883fs Pathogenic ★★ same condition
KAT6B p.Gln1194fs Pathogenic ★★ same condition
KAT6B p.Gln1321fs Pathogenic/Likely pathogenic ★★ same condition
KAT6B p.Glu1085fs Pathogenic ★★ same condition
KAT6B p.Gly1134fs Pathogenic ★★ same condition
KAT6B p.Lys1263fs 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-pro1809fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown