Is KAT6B p.Pro170= (c.510G>A) pathogenic?

KAT6B p.Pro170= (c.510G>A) is classified Benign/Likely benign in KAT6B (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-10-02). Ultra-rare (popmax 0.0401%, amr); Associated with genitopatellar syndrome.

What condition is associated with KAT6B p.Pro170= (c.510G>A)?

KAT6B p.Pro170= (c.510G>A) is associated with genitopatellar syndrome, blepharophimosis - intellectual disability syndrome, SBBYS type (ClinVar).

How common is KAT6B p.Pro170= (c.510G>A) in the general population?

KAT6B p.Pro170= (c.510G>A) is ultra-rare (popmax 0.0401%, amr) (gnomAD).

KAT6B p.Pro170=

c.510G>A · rs750020725 · VCV1660041

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0401%, amr)

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 -4.9	GERP -4.1
Overall
CADD	3.57	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0401% Admixed American · 24/59,924 alleles

Filtering AF 0.0276% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0234%

Overall 0.00229% 37/1,613,416 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0401%	2,497
Remaining individualsnot grpmax-eligible	0.0048%	20,816
East Asian	0.00223%	44,888
African / African-American	0.00133%	74,910
European (non-Finnish)	0.000678%	147,468

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.Pro170=
Coding: c.510G>A
MANE Select: NM_012330
dbSNP: rs750020725
Type: single nucleotide variant
Location: chr10:74843367 (GRCh38)
Gene constraint: LOEUF 0.098 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 49.67 · 3 PDB
Residue 170: the h15 domain

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.Pro170Arg Uncertain significance ★ ⚠ same residue
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

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-pro170 (accessed [today's date]).

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