MIPEP p.Pro42=
c.126C>T · VCV4919463
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0553%, sas)
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 -6.2 | GERP -3.2 |
| Overall | ||
| CADD | 10.56 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0553%
South Asian · 41/74,130 alleles
Filtering AF
0.0418%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0372%
Overall
0.00334%
49/1,466,288 alleles · ultra-rare
exomes 42/1,314,000 · genomes 7/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0553% | 1,808 |
| Remaining individualsnot grpmax-eligible | 0.00896% | 11,166 |
| European (non-Finnish) | 0.00027% | 370,248 |
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
- MIPEP
- Protein
- p.Pro42=
- Coding
- c.126C>T
- MANE Select
- NM_005932
- Type
- single nucleotide variant
- Location
- chr13:23889195 (GRCh38)
- Gene constraint
- LOEUF 1.181 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.33
Similar variants
- MIPEP c.1848+2T>G Likely pathogenic ★★ same type
- MIPEP p.Asp120Asn Likely pathogenic ★★ same type
- MIPEP p.Ala138Val Uncertain significance ★★ ⚠ same type
- MIPEP p.Ala570Thr Uncertain significance ★★ same type
- MIPEP p.Arg202Cys Uncertain significance ★★ same type
- MIPEP p.Arg366Cys Uncertain significance ★★ same type
- MIPEP p.Arg453His Uncertain significance ★★ ⚠ same type
- MIPEP p.Arg509His 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/mipep-p-pro42 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown