MIPEP p.Ser488=
c.1464C>T · VCV4919429
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0067%, 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 -4 | GERP -4.1 |
| Overall | ||
| CADD | 1.363 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0067%
European (non-Finnish) · 79/1,179,764 alleles
Filtering AF
0.00546%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00506%
Overall
0.00527%
85/1,613,762 alleles · very rare
exomes 78/1,461,574 · genomes 7/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0067% | 14,934 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,825 |
| Finnishnot grpmax-eligible | 0.00312% | 32,004 |
| African / African-American | 0.00133% | 74,930 |
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.Ser488=
- Coding
- c.1464C>T
- MANE Select
- NM_005932
- Type
- single nucleotide variant
- Location
- chr13:23837631 (GRCh38)
- Gene constraint
- LOEUF 1.181 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.33
- Residue 488
- a UniProt-annotated variant site (in)
Similar variants
- MIPEP p.Ser488Gly Benign ★★ same residue
- 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
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-ser488 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown