MAP2K5 p.Asp283=
c.849C>T · rs55966838 · VCV708695
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.3%, nfe)
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 Δ0.20 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.31 | GERP -3.8, phastCons 1 |
| Overall | ||
| CADD | 5.927 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.3%
European (non-Finnish) · 15,326/1,178,702 alleles
Filtering AF
1.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.28%
Overall
1.06%
17,083/1,612,470 alleles · low-frequency
exomes 15,987/1,460,198 · genomes 1,096/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.3% | 77 |
| Amishnot grpmax-eligible | 1.21% | 83 |
| Remaining individualsnot grpmax-eligible | 0.735% | 136 |
| Finnishnot grpmax-eligible | 0.719% | 139 |
| Admixed American | 0.507% | 197 |
| South Asian | 0.379% | 264 |
| African / African-American | 0.175% | 572 |
| Ashkenazi Jewishnot grpmax-eligible | 0.135% | 739 |
| Middle Eastern | 0.0661% | 1,513 |
| East Asian | 0.00669% | 14,947 |
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
- MAP2K5
- Protein
- p.Asp283=
- Coding
- c.849C>T
- MANE Select
- NM_145160
- dbSNP
- rs55966838
- Type
- single nucleotide variant
- Location
- chr15:67692480 (GRCh38)
- Gene constraint
- LOEUF 1.201 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.20 · 3 PDB
- Residue 283
- the protein kinase domain; an active site
Similar variants
- MAP2K5 c.586-8A>G Benign ★★ same type
- MAP2K5 c.1074+1G>A Uncertain significance ★ same type
- MAP2K5 p.Ala150Ser Uncertain significance ★ ⚠ same type
- MAP2K5 p.Ala157Thr Uncertain significance ★ ⚠ same type
- MAP2K5 p.Ala266Val Uncertain significance ★ ⚠ same type
- MAP2K5 p.Ala437Ser Uncertain significance ★ ⚠ same type
- MAP2K5 p.Arg125Gln Uncertain significance ★ ⚠ same type
- MAP2K5 p.Arg125Trp 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/map2k5-p-asp283 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown