Is KMT2D p.Pro493= (c.1479C>T) pathogenic?

KMT2D p.Pro493= (c.1479C>T) is classified Benign in KMT2D (ClinVar, Single submitter, 2 submitters; last evaluated 2025-07-13). Very rare (popmax 0.0022%, sas); Associated with Kabuki syndrome.

What condition is associated with KMT2D p.Pro493= (c.1479C>T)?

KMT2D p.Pro493= (c.1479C>T) is associated with Kabuki syndrome (ClinVar).

How common is KMT2D p.Pro493= (c.1479C>T) in the general population?

KMT2D p.Pro493= (c.1479C>T) is very rare (popmax 0.0022%, sas) (gnomAD).

KMT2D p.Pro493=

c.1479C>T · rs750444806 · VCV3032995

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Conditions

Kabuki 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 0.73	GERP -4.7, phastCons 0.99
Overall
CADD	7.17	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% South Asian · 2/91,056 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000137%

Overall 0.00031% 5/1,613,116 alleles · very rare exomes 5/1,461,536 · genomes 0/151,580 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0022%	45,528
European (non-Finnish)	0.000254%	393,210

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: KMT2D
Protein: p.Pro493=
Coding: c.1479C>T
MANE Select: NM_003482
dbSNP: rs750444806
Type: single nucleotide variant
Location: chr12:49052204 (GRCh38)
Gene constraint: LOEUF 0.141 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 493: a UniProt-annotated variant site (in kabuk1); the 'disordered' region; the '15 x 5 aa repeats of s/p-p-p-e/p-e/a' region

Full KMT2D gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Kabuki syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KMT2D c.10740+1G>A Pathogenic ★★ same condition
KMT2D c.14075+1G>A Pathogenic/Likely pathogenic ★★ same condition
KMT2D c.16338+2T>C Pathogenic/Likely pathogenic ★★ same condition
KMT2D c.4132-2A>G Pathogenic ★★ same condition
KMT2D c.5189-2A>G Pathogenic/Likely pathogenic ★★ same condition
KMT2D p.Arg1615Ter Pathogenic ★★ same condition
KMT2D p.Arg1903Ter Pathogenic ★★ same condition
KMT2D p.Arg2099Ter 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/kmt2d-p-pro493 (accessed [today's date]).

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