Is KAT6B p.Asp168= (c.504C>T) pathogenic?

KAT6B p.Asp168= (c.504C>T) is classified Likely benign in KAT6B (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-04-30). Ultra-rare (popmax 0.0133%, afr); Associated with genitopatellar syndrome.

What condition is associated with KAT6B p.Asp168= (c.504C>T)?

KAT6B p.Asp168= (c.504C>T) is associated with genitopatellar syndrome (ClinVar).

How common is KAT6B p.Asp168= (c.504C>T) in the general population?

KAT6B p.Asp168= (c.504C>T) is ultra-rare (popmax 0.0133%, afr) (gnomAD).

KAT6B p.Asp168=

c.504C>T · rs576505982 · VCV1198841

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, afr)

Conditions

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 -10	GERP -4.2
Overall
CADD	1.279	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0133% African / African-American · 10/74,974 alleles

Filtering AF 0.00722% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0055%

Overall 0.0013% 21/1,613,042 alleles · ultra-rare exomes 11/1,460,768 · genomes 10/152,274 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0133%	7,497
Finnishnot grpmax-eligible	0.00469%	21,307
South Asian	0.0022%	45,508
Remaining individualsnot grpmax-eligible	0.0016%	62,446
European (non-Finnish)	0.000424%	235,887

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.Asp168=
Coding: c.504C>T
MANE Select: NM_012330
dbSNP: rs576505982
Type: single nucleotide variant
Location: chr10:74843361 (GRCh38)
Gene constraint: LOEUF 0.098 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 49.67 · 3 PDB
Residue 168: the h15 domain; a β-strand

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 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
KAT6B p.Ala1317Thr Uncertain significance ★★ ⚠ same condition
KAT6B p.Ala1498Ser 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-asp168 (accessed [today's date]).

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