MAPKBP1 p.Ser322=
c.966C>T · VCV3671546
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0437%, 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 -1.4 | GERP -5.1 |
| Overall | ||
| CADD | 6.427 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0437%
European (non-Finnish) · 512/1,172,716 alleles
Filtering AF
0.0405%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0392%
Overall
0.0345%
552/1,599,314 alleles · ultra-rare
exomes 513/1,446,990 · genomes 39/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0437% | 2,290 |
| Finnishnot grpmax-eligible | 0.0282% | 3,550 |
| Remaining individualsnot grpmax-eligible | 0.0178% | 5,618 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0104% | 9,603 |
| African / African-American | 0.00538% | 18,575 |
| Admixed American | 0.0035% | 28,578 |
| South Asian | 0.00224% | 44,589 |
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.Ser322=
- Coding
- c.966C>T
- MANE Select
- NM_014994
- Type
- single nucleotide variant
- Location
- chr15:41813767 (GRCh38)
- Gene constraint
- LOEUF 0.484 · pLI 0.84 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 62.82
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-ser322 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown