Is KAT6B p.Pro77fs (c.230del) pathogenic?

KAT6B p.Pro77fs (c.230del) is classified Uncertain significance in KAT6B (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-09). No gnomAD frequency available for this variant; Associated with genitopatellar syndrome.

What condition is associated with KAT6B p.Pro77fs (c.230del)?

KAT6B p.Pro77fs (c.230del) is associated with genitopatellar syndrome (ClinVar).

How common is KAT6B p.Pro77fs (c.230del) in the general population?

KAT6B p.Pro77fs (c.230del) is no gnomAD frequency available for this variant (gnomAD).

KAT6B p.Pro77fs

c.230del · rs2548334026 · VCV2015064

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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	predicted	premature termination codon in exon 3 of 18
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.1, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: KAT6B
Protein: p.Pro77fs
Coding: c.230del
MANE Select: NM_012330
dbSNP: rs2548334026
Type: Deletion
Location: chr10:74843085 (GRCh38)
Gene constraint: LOEUF 0.098 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 49.67 · 3 PDB
Residue 77: the samd1-like winged helix (wh) domain; the 'disordered' 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

Similar variants

KAT6B p.Gln1194fs Pathogenic ★★ same condition
KAT6B p.Lys1263fs Pathogenic ★★ same condition
KAT6B p.Arg1797_Met1798del Uncertain significance ★★ same condition
KAT6B p.Glu1087_Glu1089del Uncertain significance ★★ same condition
KAT6B p.Thr1534del Uncertain significance ★★ same condition
KAT6B c.731-11del Benign/Likely benign ★★ same condition
KAT6B p.Ala1331fs Pathogenic ★ same condition
KAT6B p.Ala1621fs 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-pro77fs (accessed [today's date]).

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