KMT2B p.Pro620=
c.1860T>C · rs879561764 · VCV1232075
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.613%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -2.5, phastCons 0.001 |
| Overall | ||
| CADD | 2.484 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.613%
Admixed American · 186/30,362 alleles
Filtering AF
0.541%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.513%
Overall
0.207%
2,036/981,528 alleles · rare
exomes 1,559/914,388 · genomes 477/67,140 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.613% | 163 |
| African / African-American | 0.572% | 175 |
| East Asian | 0.439% | 228 |
| South Asian | 0.391% | 255 |
| Finnishnot grpmax-eligible | 0.371% | 269 |
| Remaining individualsnot grpmax-eligible | 0.293% | 341 |
| Ashkenazi Jewishnot grpmax-eligible | 0.2% | 500 |
| European (non-Finnish) | 0.147% | 682 |
| Middle Eastern | 0.107% | 937 |
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
- KMT2B
- Protein
- p.Pro620=
- Coding
- c.1860T>C
- MANE Select
- NM_014727
- dbSNP
- rs879561764
- Type
- single nucleotide variant
- Location
- chr19:35721207 (GRCh38)
- Gene constraint
- LOEUF 0.127 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 620
- the 'disordered' region; a UniProt-annotated variant site (in dyt28)
Similar variants
- KMT2B p.Ala1616Val Likely pathogenic ★★ same type
- KMT2B p.Ala2641Thr Likely pathogenic ★★ same type
- KMT2B p.Arg142Ter Pathogenic ★★ same type
- KMT2B p.Arg1597Trp Pathogenic/Likely pathogenic ★★ same type
- KMT2B p.Arg1705Ter Pathogenic ★★ same type
- KMT2B p.Arg2565Gly Likely pathogenic ★★ same type
- KMT2B p.Arg2610Cys Likely pathogenic ★★ same type
- KMT2B p.Arg545Ter 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/kmt2b-p-pro620 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown