Is KAT2B p.Lys599= (c.1797G>A) pathogenic?

KAT2B p.Lys599= (c.1797G>A) is classified Likely benign in KAT2B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-07-08). Rare (popmax 0.14%, afr); Associated with KAT2B-related disorder.

What condition is associated with KAT2B p.Lys599= (c.1797G>A)?

KAT2B p.Lys599= (c.1797G>A) is associated with KAT2B-related disorder (ClinVar).

How common is KAT2B p.Lys599= (c.1797G>A) in the general population?

KAT2B p.Lys599= (c.1797G>A) is rare (popmax 0.14%, afr) (gnomAD).

KAT2B p.Lys599=

c.1797G>A · rs141010149 · VCV3045525

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.14%, afr)

Conditions

KAT2B-related disorder

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 0.58	GERP -1.4, phastCons 0.91
Overall
CADD	6.306	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.14% African / African-American · 105/74,990 alleles

Filtering AF 0.118% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.11%

Overall 0.00726% 117/1,611,356 alleles · rare exomes 55/1,459,064 · genomes 62/152,292 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.14%	714
Admixed American	0.01%	10,004
Remaining individualsnot grpmax-eligible	0.00801%	12,477
European (non-Finnish)	8.49e-05%	1,177,670

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: KAT2B
Protein: p.Lys599=
Coding: c.1797G>A
MANE Select: NM_003884
dbSNP: rs141010149
Type: single nucleotide variant
Location: chr3:20136989 (GRCh38)
Gene constraint: LOEUF 0.461 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 78.22 · 25 PDB
Residue 599: the n-acetyltransferase domain; an α-helix

Full KAT2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

KAT2B-related disorder

Similar variants

KAT2B p.Ile764Val Uncertain significance ★ ⚠ same condition
KAT2B p.Ala466Val Uncertain significance ⚠ same condition
KAT2B p.Gly208Ala Uncertain significance ⚠ same condition
KAT2B p.Ser434Cys Uncertain significance ⚠ same condition
KAT2B c.2157-5T>C Likely benign same condition
KAT2B c.670-3A>C Likely benign same condition
KAT2B c.852-5C>T Likely benign same condition
KAT2B p.Ala144= Likely benign 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/kat2b-p-lys599 (accessed [today's date]).

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