KMT2C p.Pro685=
c.2055A>G · rs182979631 · VCV1653867
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.181%, afr)
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 -5.1 | GERP -1.3 |
| Overall | ||
| CADD | 0.252 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.181%
African / African-American · 136/75,048 alleles
Filtering AF
0.156%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.147%
Overall
0.00911%
147/1,614,086 alleles · rare
exomes 66/1,461,754 · genomes 81/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.181% | 552 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,928 |
| Admixed American | 0.00167% | 60,000 |
| European (non-Finnish) | 0.000254% | 393,326 |
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
- KMT2C
- Protein
- p.Pro685=
- Coding
- c.2055A>G
- MANE Select
- NM_170606
- dbSNP
- rs182979631
- Type
- single nucleotide variant
- Location
- chr7:152248379 (GRCh38)
- Gene constraint
- LOEUF 0.202 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 685
- a UniProt-annotated variant site (in klefs2)
Similar variants
- 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
- KMT2C p.Arg2610Ter Pathogenic/Likely pathogenic ★★ same type
- KMT2C p.Arg3079Ter 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-pro685 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown