KMT2A p.Pro562=
c.1686T>G · rs2496802724 · VCV2057603
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -3.6 | GERP -0.98 |
| Overall | ||
| CADD | 1.857 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- KMT2A
- Protein
- p.Pro562=
- Coding
- c.1686T>G
- MANE Select
- NM_001197104
- dbSNP
- rs2496802724
- Type
- single nucleotide variant
- Location
- chr11:118472845 (GRCh38)
- Gene constraint
- LOEUF 0.065 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 562
- the 'disordered' region
Similar variants
- 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
- KMT2A p.Arg1101Ter Pathogenic/Likely 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-pro562 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown