KMT2C p.Arg2139=
c.6417A>T · rs2129119970 · VCV2658215
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
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 -2 | GERP -4.5 |
| Overall | ||
| CADD | 1.585 | 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
- KMT2C
- Protein
- p.Arg2139=
- Coding
- c.6417A>T
- MANE Select
- NM_170606
- dbSNP
- rs2129119970
- Type
- single nucleotide variant
- Location
- chr7:152181443 (GRCh38)
- Gene constraint
- LOEUF 0.202 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 2139
- a UniProt-annotated variant site (in klefs2); the 'disordered' region
Similar variants
- KMT2C p.Arg2139Ter Likely pathogenic ★ same residue
- KMT2C p.Arg2139Gln Uncertain significance ★ ⚠ same residue
- KMT2C c.1013-1G>A Pathogenic/Likely pathogenic ★★ same type
- KMT2C c.14344-1G>A Pathogenic/Likely pathogenic ★★ same type
- KMT2C p.Arg1481Ter Pathogenic/Likely pathogenic ★★ same type
- KMT2C p.Arg1906Ter Pathogenic ★★ same type
- KMT2C p.Arg2066Ter Pathogenic ★★ same type
- KMT2C p.Arg2609Ter 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/kmt2c-p-arg2139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown