MAP3K20 p.Pro782=
c.2346C>T · rs746871474 · VCV1635451
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00444%, nfe)
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 -5.4 | GERP -5.7 |
| Overall | ||
| CADD | 0.315 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00444%
European (non-Finnish) · 52/1,171,558 alleles
Filtering AF
0.00345%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00312%
Overall
0.00351%
56/1,595,676 alleles · very rare
exomes 50/1,444,196 · genomes 6/151,480 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00444% | 22,530 |
| East Asian | 0.00226% | 44,248 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,592 |
| Finnishnot grpmax-eligible | 0.00159% | 62,848 |
| South Asian | 0.00113% | 88,834 |
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.Pro782=
- Coding
- c.2346C>T
- MANE Select
- NM_016653
- dbSNP
- rs746871474
- Type
- single nucleotide variant
- Location
- chr2:173266693 (GRCh38)
- Gene constraint
- LOEUF 0.569 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 69.15 · 8 PDB
- Residue 782
- a UniProt-annotated variant site (in cnm6; decrease of protein abundance); the 'disordered' region; the 'c-terminal domain (ctd)' region
Similar variants
- 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
- MAP3K20 p.Gln632Ter Uncertain significance ★★ same type
- MAP3K20 p.Glu405Gly 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-pro782 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown