MPO p.Asn299=
c.897T>C · VCV4936170
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.149%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.59 | GERP -4.7 |
| Overall | ||
| CADD | 2.887 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.149%
South Asian · 136/91,074 alleles
Filtering AF
0.129%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.121%
Overall
0.00906%
145/1,601,284 alleles · rare
exomes 137/1,449,038 · genomes 8/152,246 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.149% | 670 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,918 |
| Admixed American | 0.00167% | 60,006 |
| European (non-Finnish) | 8.48e-05% | 1,179,906 |
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
- MPO
- Protein
- p.Asn299=
- Coding
- c.897T>C
- MANE Select
- NM_000250
- Type
- single nucleotide variant
- Location
- chr17:58278134 (GRCh38)
- Gene constraint
- LOEUF 0.992 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.55 · 49 PDB
Similar variants
- MPO p.Asn299Ser Uncertain significance ★ ⚠ same residue
- MPO p.Gln241Ter Pathogenic/Likely pathogenic ★★ same type
- MPO p.Trp602Ter Likely pathogenic ★★ same type
- MPO p.Arg691Gln Uncertain significance ★★ ⚠ same type
- MPO p.Met356Val Uncertain significance ★★ ⚠ same type
- MPO c.2031-6A>C Benign ★★ same type
- MPO p.Arg604Cys Likely benign ★★ ⚠ same type
- MPO p.Asn729= Benign/Likely benign ★★ 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/mpo-p-asn299 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown