MAPK8IP3 p.Glu3=
c.9G>A · rs139282045 · VCV1675598
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.868%, 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 5.5 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 12.83 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.868%
European (non-Finnish) · 10,136/1,167,660 alleles
Filtering AF
0.854%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.848%
Overall
0.699%
11,098/1,586,738 alleles · rare
exomes 10,367/1,434,442 · genomes 731/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.868% | 115 |
| Finnishnot grpmax-eligible | 0.72% | 139 |
| Remaining individualsnot grpmax-eligible | 0.453% | 221 |
| Admixed American | 0.266% | 376 |
| African / African-American | 0.114% | 874 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0344% | 2,907 |
| Middle Eastern | 0.0168% | 5,940 |
| South Asian | 0.0125% | 8,023 |
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
- MAPK8IP3
- Protein
- p.Glu3=
- Coding
- c.9G>A
- MANE Select
- NM_001318852
- dbSNP
- rs139282045
- Type
- single nucleotide variant
- Location
- chr16:1706348 (GRCh38)
- Gene constraint
- LOEUF 0.407 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.19 · 5 PDB
Similar variants
- MAPK8IP3 p.Arg1147Cys Pathogenic/Likely pathogenic ★★ same type
- MAPK8IP3 p.Arg579Cys Pathogenic/Likely pathogenic ★★ same type
- MAPK8IP3 p.Gln468Ter Pathogenic/Likely pathogenic ★★ same type
- MAPK8IP3 p.Glu27Ter Likely pathogenic ★★ same type
- MAPK8IP3 p.Glu462Gly Likely pathogenic ★★ same type
- MAPK8IP3 p.Leu445Pro Likely pathogenic ★★ same type
- MAPK8IP3 p.Tyr37Ter Likely pathogenic ★★ same type
- MAPK8IP3 c.1898+5G>A 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/mapk8ip3-p-glu3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown