MAPK13 p.Thr112=
c.336G>A · rs61730659 · VCV785169
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.39%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.22 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.4 | |
| Overall | ||
| CADD | 10.39 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.39%
African / African-American · 1,046/75,036 alleles
Filtering AF
1.32%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.3%
Overall
0.0722%
1,165/1,613,684 alleles · low-frequency
exomes 558/1,461,384 · genomes 607/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.39% | 72 |
| Admixed American | 0.0883% | 1,132 |
| Remaining individualsnot grpmax-eligible | 0.088% | 1,136 |
| Middle Eastern | 0.033% | 3,028 |
| East Asian | 0.00446% | 22,441 |
| South Asian | 0.0011% | 91,028 |
| European (non-Finnish) | 0.000509% | 196,610 |
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
- MAPK13
- Protein
- p.Thr112=
- Coding
- c.336G>A
- MANE Select
- NM_002754
- dbSNP
- rs61730659
- Type
- single nucleotide variant
- Location
- chr6:36135780 (GRCh38)
- Gene constraint
- LOEUF 0.906 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.14 · 8 PDB
- Residue 112
- the protein kinase domain; a β-strand
Similar variants
- MAPK13 p.Thr112Met Uncertain significance ★ ⚠ same residue
- MAPK13 p.Ala281Gly Uncertain significance ★ ⚠ same type
- MAPK13 p.Ala302Thr Uncertain significance ★ ⚠ same type
- MAPK13 p.Ala320Ser Uncertain significance ★ ⚠ same type
- MAPK13 p.Arg276Trp Uncertain significance ★ ⚠ same type
- MAPK13 p.Arg296His Uncertain significance ★ ⚠ same type
- MAPK13 p.Arg354Gln Uncertain significance ★ ⚠ same type
- MAPK13 p.Arg354Trp 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/mapk13-p-thr112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown