MAPKBP1 p.Pro953=
c.2859G>A · rs141865866 · VCV716220
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.18%, afr)
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 -2.3 | GERP -4.8 |
| Overall | ||
| CADD | 2.241 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.18%
African / African-American · 886/74,980 alleles
Filtering AF
1.12%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.09%
Overall
0.0812%
1,311/1,613,952 alleles · low-frequency
exomes 767/1,461,800 · genomes 544/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.18% | 85 |
| Middle Eastern | 0.348% | 287 |
| Admixed American | 0.148% | 674 |
| Remaining individualsnot grpmax-eligible | 0.125% | 801 |
| European (non-Finnish) | 0.019% | 5,268 |
| South Asian | 0.00988% | 10,118 |
| East Asian | 0.00669% | 14,953 |
| Finnishnot grpmax-eligible | 0.00156% | 64,028 |
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
- MAPKBP1
- Protein
- p.Pro953=
- Coding
- c.2859G>A
- MANE Select
- NM_014994
- dbSNP
- rs141865866
- Type
- single nucleotide variant
- Location
- chr15:41821724 (GRCh38)
- Gene constraint
- LOEUF 0.484 · pLI 0.84 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 62.82
- Residue 953
- the 'disordered' region
Similar variants
- MAPKBP1 c.1711+5G>A Uncertain significance ★★ same type
- MAPKBP1 p.Ala1126Pro Uncertain significance ★★ ⚠ same type
- MAPKBP1 p.Ala1407Thr Uncertain significance ★★ ⚠ same type
- MAPKBP1 p.Ala1427Ser Uncertain significance ★★ ⚠ same type
- MAPKBP1 p.Ala146Thr Uncertain significance ★★ ⚠ same type
- MAPKBP1 p.Arg1102Cys Uncertain significance ★★ ⚠ same type
- MAPKBP1 p.Arg1314Trp Uncertain significance ★★ ⚠ same type
- MAPKBP1 p.Arg1337Ser 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/mapkbp1-p-pro953 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown