Is KMT2D p.Ser1007fs (c.3019_3020del) pathogenic?

KMT2D p.Ser1007fs (c.30193020del) is classified Likely pathogenic in KMT2D (ClinVar, Single submitter, 1 submitter; last evaluated 2016-11-01). No gnomAD frequency available for this variant; Associated with Kabuki syndrome 1.

What condition is associated with KMT2D p.Ser1007fs (c.3019_3020del)?

KMT2D p.Ser1007fs (c.3019_3020del) is associated with Kabuki syndrome 1 (ClinVar).

How common is KMT2D p.Ser1007fs (c.3019_3020del) in the general population?

KMT2D p.Ser1007fs (c.3019_3020del) is no gnomAD frequency available for this variant (gnomAD).

KMT2D p.Ser1007fs

c.3019_3020del · rs1555196459 · VCV547413

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Kabuki syndrome 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 12 of 55
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.5	GERP 0.78, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: KMT2D
Protein: p.Ser1007fs
Coding: c.3019_3020del
MANE Select: NM_003482
dbSNP: rs1555196459
Type: Deletion
Location: chr12:49050568 (GRCh38)
Gene constraint: LOEUF 0.141 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 1007: a UniProt-annotated variant site (in kabuk1); the 'disordered' region

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

Disease context

Kabuki syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KMT2D c.3907-2_3907-1del Pathogenic ★★ same condition
KMT2D p.Ala3808fs Pathogenic/Likely pathogenic ★★ same condition
KMT2D p.Arg2460fs Pathogenic ★★ same condition
KMT2D p.Arg4666fs Pathogenic/Likely pathogenic ★★ same condition
KMT2D p.Arg845fs Pathogenic ★★ same condition
KMT2D p.Asn5480fs Pathogenic ★★ same condition
KMT2D p.Asp1876fs Pathogenic/Likely pathogenic ★★ same condition
KMT2D p.Gln3796fs 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-ser1007fs (accessed [today's date]).

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