MAPKAP1 p.Thr456=
c.1368G>A · rs35549826 · VCV790626
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.59%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.308 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -7.2 | GERP -4.2 |
| Overall | ||
| CADD | 6.755 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.59%
African / African-American · 1,191/75,036 alleles
Filtering AF
1.51%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.48%
Overall
0.0861%
1,389/1,613,468 alleles · low-frequency
exomes 719/1,461,134 · genomes 670/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.59% | 63 |
| Admixed American | 0.137% | 731 |
| Remaining individualsnot grpmax-eligible | 0.11% | 905 |
| Middle Eastern | 0.033% | 3,031 |
| European (non-Finnish) | 0.00373% | 26,809 |
| South Asian | 0.0011% | 90,996 |
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
- MAPKAP1
- Protein
- p.Thr456=
- Coding
- c.1368G>A
- MANE Select
- NM_001006617
- dbSNP
- rs35549826
- Type
- single nucleotide variant
- Location
- chr9:125444576 (GRCh38)
- Gene constraint
- LOEUF 0.369 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.55 · 23 PDB
- Residue 456
- the sin1-type ph domain; a β-strand
Similar variants
- MAPKAP1 p.Ser488= Benign ★★ same type
- MAPKAP1 p.Ala201Thr Uncertain significance ★ ⚠ same type
- MAPKAP1 p.Ala229Asp Uncertain significance ★ same type
- MAPKAP1 p.Ala286Thr Uncertain significance ★ ⚠ same type
- MAPKAP1 p.Arg15Gln Uncertain significance ★ ⚠ same type
- MAPKAP1 p.Arg202Lys Uncertain significance ★ ⚠ same type
- MAPKAP1 p.Arg503Ile Uncertain significance ★ ⚠ same type
- MAPKAP1 p.Asn476Ser 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/mapkap1-p-thr456 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown