KMT2C p.Asn1663fs
c.4986del · VCV4856819
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
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 33 of 59 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP 3.1, phastCons 0.13 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- KMT2C
- Protein
- p.Asn1663fs
- Coding
- c.4986del
- MANE Select
- NM_170606
- Type
- Deletion
- Location
- chr7:152187284 (GRCh38)
- Gene constraint
- LOEUF 0.202 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 1663
- a UniProt-annotated variant site (in klefs2)
Similar variants
- KMT2C c.1185-20_1185-7del Pathogenic ★★ same type
- KMT2C p.Arg490fs Pathogenic ★★ same type
- KMT2C p.Asn2848fs Pathogenic ★★ same type
- KMT2C p.His2950fs Pathogenic ★★ same type
- KMT2C p.Leu1155_Val1156insTer Pathogenic ★★ same type
- KMT2C p.Thr610fs Pathogenic ★★ same type
- KMT2C c.162-7del Benign/Likely benign ★★ same type
- KMT2C c.1622-6del Likely benign ★★ 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/kmt2c-p-asn1663fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown