MIPEP p.Phe543=
c.1629T>C · rs766331932 · VCV1653420
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 1.3 | GERP -2.6, phastCons 1 |
| Overall | ||
| CADD | 6.606 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,050 alleles
Filtering AF
0.00556%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00399%
Overall
0.00081%
13/1,604,572 alleles · ultra-rare
exomes 12/1,452,396 · genomes 1/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,050 |
| Admixed American | 0.012% | 8,349 |
| African / African-American | 0.00134% | 74,436 |
| South Asian | 0.00113% | 88,526 |
| European (non-Finnish) | 0.000255% | 392,103 |
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.Phe543=
- Coding
- c.1629T>C
- MANE Select
- NM_005932
- dbSNP
- rs766331932
- Type
- single nucleotide variant
- Location
- chr13:23836264 (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-phe543 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown