MAP3K20 p.Ser565=
c.1695C>T · rs772234268 · VCV1643116
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0347%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.51 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.4 | GERP -5.4 |
| Overall | ||
| CADD | 5.558 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0347%
South Asian · 31/89,380 alleles
Filtering AF
0.0251%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0218%
Overall
0.00286%
46/1,607,118 alleles · ultra-rare
exomes 45/1,454,984 · genomes 1/152,134 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0347% | 2,883 |
| Middle Eastern | 0.0165% | 6,062 |
| East Asian | 0.00223% | 44,820 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,260 |
| Finnishnot grpmax-eligible | 0.00156% | 63,956 |
| African / African-American | 0.00134% | 74,438 |
| European (non-Finnish) | 0.000849% | 117,828 |
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.Ser565=
- Coding
- c.1695C>T
- MANE Select
- NM_016653
- dbSNP
- rs772234268
- Type
- single nucleotide variant
- Location
- chr2:173263888 (GRCh38)
- Gene constraint
- LOEUF 0.569 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 69.15 · 8 PDB
- Residue 565
- a UniProt-annotated variant site (in cnm6; decrease of protein abundance)
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-ser565 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown