MIPEP p.Arg517=
c.1549A>C · rs371176915 · VCV2068132
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00963%, 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 2.8 | GERP 0.12, phastCons 1 |
| Overall | ||
| CADD | 6.027 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00963%
European (non-Finnish) · 112/1,162,878 alleles
Filtering AF
0.00816%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00763%
Overall
0.00753%
118/1,567,926 alleles · very rare
exomes 104/1,415,960 · genomes 14/151,966 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00963% | 10,383 |
| African / African-American | 0.00555% | 18,025 |
| Remaining individualsnot grpmax-eligible | 0.00331% | 30,207 |
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.Arg517=
- Coding
- c.1549A>C
- MANE Select
- NM_005932
- dbSNP
- rs371176915
- Type
- single nucleotide variant
- Location
- chr13:23836344 (GRCh38)
- Gene constraint
- LOEUF 1.181 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.33
Similar variants
- MIPEP p.Arg517Gly Uncertain significance ★ ⚠ 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-arg517 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown