MAP3K1 p.Arg790=
c.2370G>A · rs765882456 · VCV3044726
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00375%, nfe)
Conditions
1
MAP3K1-related disorder
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 5.9 | GERP 2.4, phastCons 1 |
| Overall | ||
| CADD | 15.46 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00375%
European (non-Finnish) · 44/1,174,480 alleles
Filtering AF
0.00284%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00253%
Overall
0.00286%
46/1,607,028 alleles · very rare
exomes 42/1,455,134 · genomes 4/151,894 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00375% | 26,693 |
| East Asian | 0.00223% | 44,880 |
| African / African-American | 0.00134% | 74,700 |
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
- MAP3K1
- Protein
- p.Arg790=
- Coding
- c.2370G>A
- MANE Select
- NM_005921
- dbSNP
- rs765882456
- Type
- single nucleotide variant
- Location
- chr5:56881570 (GRCh38)
- Gene constraint
- LOEUF 0.355 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.80 · 1 PDB
- Residue 790
- an α-helix
Disease context
MAP3K1-related disorder
Similar variants
- MAP3K1 p.Leu189Pro Pathogenic ★ ⚠ same condition
- MAP3K1 p.Leu189Val Likely pathogenic ★ ⚠ same condition
- MAP3K1 p.Arg1509His Uncertain significance ⚠ same condition
- MAP3K1 p.Thr603Ile Uncertain significance ⚠ same condition
- MAP3K1 p.Val579Met Uncertain significance ⚠ same condition
- MAP3K1 p.Thr1400= Likely benign same condition
- MAP3K1 p.Arg186Gly Pathogenic/Likely pathogenic ★★ ⚠ same type
- MAP3K1 p.Ala594Ser 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/map3k1-p-arg790 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown