Is KMT2D p.Pro55Ser (c.163C>T) pathogenic?

KMT2D p.Pro55Ser (c.163C>T) is classified Benign in KMT2D (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-17). AlphaMissense: likely benign (0.0665); Very rare (popmax 0.00801%, afr); Associated with Kabuki syndrome.

What condition is associated with KMT2D p.Pro55Ser (c.163C>T)?

KMT2D p.Pro55Ser (c.163C>T) is associated with Kabuki syndrome (ClinVar).

How common is KMT2D p.Pro55Ser (c.163C>T) in the general population?

KMT2D p.Pro55Ser (c.163C>T) is very rare (popmax 0.00801%, afr) (gnomAD).

What do computational predictors say about KMT2D p.Pro55Ser (c.163C>T)?

AlphaMissense predicts likely benign (score 0.0665) — an in-silico prediction, not a clinical call.

KMT2D p.Pro55Ser

c.163C>T · rs1314970592 · VCV1485311

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0665 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00801%, afr)

Conditions

Kabuki syndrome

Computational evidence

Protein change
AlphaMissense	0.0665	likely benign
REVEL	0.393	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.5	GERP -1.7, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 779 bp · p 0.092 · regional, not allelic
Overall
CADD	12.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00801% African / African-American · 6/74,892 alleles

Filtering AF 0.00347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00229%

Overall 0.000434% 7/1,613,784 alleles · very rare exomes 6/1,461,642 · genomes 1/152,142 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00801%	12,482
Admixed American	0.00167%	59,994

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.Pro55Ser
Coding: c.163C>T
MANE Select: NM_003482
dbSNP: rs1314970592
Type: single nucleotide variant
Location: chr12:49054913 (GRCh38)
Gene constraint: LOEUF 0.141 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 55: the 'disordered' 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-pro55ser (accessed [today's date]).

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