MPI c.1054del
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 6.2e-05%)
Conditions
1
MPI-congenital disorder of glycosylation
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.4, phastCons 1 |
| Non-coding constraint | Z 3.25 | 1 kb window · o/e 0.79 · regional · uncalibrated |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.2e-05%
Overall
6.2e-05%
1/1,613,894 alleles · very rare
exomes 1/1,461,624 · genomes 0/152,270 · joint denominator
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
- MPI
- Coding
- c.1054del
- MANE Select
- NM_002435
- dbSNP
- rs752976348
- Type
- Deletion
- Location
- chr15:74897511 (GRCh38)
- Gene constraint
- LOEUF 1.04 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.50
Disease context
MPI-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor MPI-CDG (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- MPI c.845-2del Likely pathogenic ★★ same condition
- MPI p.Ala277fs Pathogenic/Likely pathogenic ★★ same condition
- MPI p.Ala363fs Pathogenic/Likely pathogenic ★★ same condition
- MPI p.Arg29fs Pathogenic/Likely pathogenic ★★ same condition
- MPI p.Glu166fs Likely pathogenic ★★ same condition
- MPI p.Glu211fs Pathogenic/Likely pathogenic ★★ same condition
- MPI p.Glu331fs Pathogenic/Likely pathogenic ★★ same condition
- MPI p.Ile220fs Pathogenic/Likely pathogenic ★★ same condition
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/mpi-c-1054del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown