Is KMT2A p.Asp2003= (c.6009C>T) pathogenic?

KMT2A p.Asp2003= (c.6009C>T) is classified Benign/Likely benign in KMT2A (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-28). Rare (popmax 0.33%, mid).

How common is KMT2A p.Asp2003= (c.6009C>T) in the general population?

KMT2A p.Asp2003= (c.6009C>T) is rare (popmax 0.33%, mid) (gnomAD).

KMT2A p.Asp2003=

c.6009C>T · rs77421119 · VCV774701

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.33%, mid)

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 0.002	GERP -0.16, phastCons 0.79
Overall
CADD	7.527	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.33% Middle Eastern · 20/6,062 alleles

Filtering AF 0.219% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.183%

Overall 0.102% 1,640/1,613,990 alleles · rare exomes 1,503/1,461,676 · genomes 137/152,314 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.33%	303
Remaining individualsnot grpmax-eligible	0.12%	833
European (non-Finnish)	0.116%	864
South Asian	0.103%	969
Admixed American	0.0833%	1,201
Finnishnot grpmax-eligible	0.0437%	2,287
African / African-American	0.008%	12,505
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,608

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: KMT2A
Protein: p.Asp2003=
Coding: c.6009C>T
MANE Select: NM_001197104
dbSNP: rs77421119
Type: single nucleotide variant
Location: chr11:118499350 (GRCh38)
Gene constraint: LOEUF 0.065 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)

Full KMT2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

KMT2A p.Asp2003Asn Uncertain significance ★ same residue
KMT2A c.10835+1G>A Likely pathogenic ★★ same type
KMT2A c.11071+1G>A Pathogenic ★★ same type
KMT2A c.4012+1G>C Pathogenic ★★ same type
KMT2A c.502+1G>A Pathogenic ★★ same type
KMT2A c.6079+2T>C Likely pathogenic ★★ same type
KMT2A p.Arg1064Ter Pathogenic ★★ same type
KMT2A p.Arg1081Ter Pathogenic ★★ same type

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-asp2003 (accessed [today's date]).

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