MAP3K20 p.Arg580=
c.1740G>A · rs887828006 · VCV2187352
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00938%, afr)
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 0.15 | GERP -5.5, phastCons 0.68 |
| Overall | ||
| CADD | 6.728 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00938%
African / African-American · 7/74,642 alleles
Filtering AF
0.00439%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0031%
Overall
0.000627%
10/1,595,182 alleles · very rare
exomes 6/1,443,052 · genomes 4/152,130 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00938% | 10,663 |
| Remaining individualsnot grpmax-eligible | 0.00323% | 30,926 |
| Admixed American | 0.00176% | 56,832 |
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
- MAP3K20
- Protein
- p.Arg580=
- Coding
- c.1740G>A
- MANE Select
- NM_016653
- dbSNP
- rs887828006
- Type
- single nucleotide variant
- Location
- chr2:173266087 (GRCh38)
- Gene constraint
- LOEUF 0.569 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 69.15 · 8 PDB
- Residue 580
- a UniProt-annotated variant site (in cnm6; decrease of protein abundance); a UniProt-annotated variant site (in)
Similar variants
- MAP3K20 p.Arg580Gln Uncertain significance ★ ⚠ same residue
- MAP3K20 p.Arg580Pro Uncertain significance ★ ⚠ same residue
- MAP3K20 p.Arg250Trp Uncertain significance ★★ ⚠ same type
- MAP3K20 p.Arg293Lys Uncertain significance ★★ same type
- MAP3K20 p.Arg536Lys Uncertain significance ★★ ⚠ same type
- MAP3K20 p.Arg634Gly Uncertain significance ★★ ⚠ same type
- MAP3K20 p.Arg774Trp Uncertain significance ★★ ⚠ same type
- MAP3K20 p.Arg795His Uncertain significance ★★ ⚠ 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/map3k20-p-arg580 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown