Is KMT2A p.Pro103fs (c.308del) pathogenic?

KMT2A p.Pro103fs (c.308del) is classified Pathogenic in KMT2A (ClinVar, Single submitter, 1 submitter; last evaluated 2018-02-13). Absent from gnomAD; Associated with Inborn genetic diseases.

What condition is associated with KMT2A p.Pro103fs (c.308del)?

KMT2A p.Pro103fs (c.308del) is associated with Inborn genetic diseases (ClinVar).

How common is KMT2A p.Pro103fs (c.308del) in the general population?

KMT2A p.Pro103fs (c.308del) is absent from gnomAD (gnomAD).

KMT2A p.Pro103fs

c.308del · rs1949193924 · VCV985912

Pathogenic Single submitter

Classification

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

Inborn genetic diseases

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 1 of 36
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.3	GERP 1.4, 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: KMT2A
Protein: p.Pro103fs
Coding: c.308del
MANE Select: NM_001197104
dbSNP: rs1949193924
Type: Deletion
Location: chr11:118436819 (GRCh38)
Gene constraint: LOEUF 0.065 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 103: the 'disordered' region

Full KMT2A 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

KMT2A p.Arg1154_Gly1156del Pathogenic ★★ same condition
KMT2A p.Arg1930fs Pathogenic ★★ same condition
KMT2A p.Pro773fs Pathogenic ★★ same condition
KMT2A p.Ala2117fs Pathogenic ★ same condition
KMT2A p.Ala2671fs Pathogenic ★ same condition
KMT2A p.Asn968fs Pathogenic ★ same condition
KMT2A p.Gly2169fs Pathogenic ★ same condition
KMT2A p.Lys1343fs 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/kmt2a-p-pro103fs (accessed [today's date]).

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