KMT2A p.Leu1663Ter
c.4988T>A · rs1565294188 · VCV620186
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
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. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 15 of 36 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 38.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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.Leu1663Ter
- Coding
- c.4988T>A
- MANE Select
- NM_001197104
- dbSNP
- rs1565294188
- Type
- single nucleotide variant
- Location
- chr11:118491912 (GRCh38)
- Gene constraint
- LOEUF 0.065 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 1663
- the 'disordered' region; the bromo domain
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-leu1663ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown