Is KAT6A p.Pro1747= (c.5241A>G) pathogenic?

KAT6A p.Pro1747= (c.5241A>G) is classified Benign/Likely benign in KAT6A (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-09-29). Rare (popmax 0.129%, afr); Associated with Inborn genetic diseases.

What condition is associated with KAT6A p.Pro1747= (c.5241A>G)?

KAT6A p.Pro1747= (c.5241A>G) is associated with Inborn genetic diseases (ClinVar).

How common is KAT6A p.Pro1747= (c.5241A>G) in the general population?

KAT6A p.Pro1747= (c.5241A>G) is rare (popmax 0.129%, afr) (gnomAD).

KAT6A p.Pro1747=

c.5241A>G · rs140894504 · VCV1262345

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.129%, afr)

Conditions

Inborn genetic diseases

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 -7.3	GERP -5.3
Overall
CADD	0.571	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.129% African / African-American · 97/75,030 alleles

Filtering AF 0.108% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.101%

Overall 0.00762% 123/1,614,076 alleles · rare exomes 67/1,461,862 · genomes 56/152,214 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.129%	774
Middle Eastern	0.0495%	2,021
Remaining individualsnot grpmax-eligible	0.0224%	4,465
Admixed American	0.00833%	12,004
South Asian	0.0022%	45,534
European (non-Finnish)	0.000169%	589,991

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: KAT6A
Protein: p.Pro1747=
Coding: c.5241A>G
MANE Select: NM_006766
dbSNP: rs140894504
Type: single nucleotide variant
Location: chr8:41932979 (GRCh38)
Gene constraint: LOEUF 0.083 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 49.12 · 21 PDB

Full KAT6A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KAT6A p.Arg1129Ter Pathogenic ★★ same condition
KAT6A p.Arg148Ter Pathogenic ★★ same condition
KAT6A p.Arg286Ter Pathogenic ★★ same condition
KAT6A p.Arg735Ter Pathogenic ★★ same condition
KAT6A p.Ala1451Gly Uncertain significance ★★ ⚠ same condition
KAT6A p.Ala492Val Uncertain significance ★★ ⚠ same condition
KAT6A p.Arg1086Ser Uncertain significance ★★ ⚠ same condition
KAT6A p.Asn1898Ser 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/kat6a-p-pro1747 (accessed [today's date]).

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