MIPEP p.His670=
c.2010C>T · VCV4705277
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00878%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.485 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.20 | donor loss, 34 bp away · masked 0 · deltas |
| Constraint at this position | ||
| Conservation | phyloP -4.6 | GERP -3.8 |
| Overall | ||
| CADD | 1.318 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00878%
South Asian · 8/91,086 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00312%
Overall
0.00143%
23/1,613,728 alleles · very rare
exomes 22/1,461,518 · genomes 1/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00878% | 11,386 |
| Admixed American | 0.00167% | 60,000 |
| African / African-American | 0.00133% | 74,930 |
| European (non-Finnish) | 0.0011% | 90,771 |
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.His670=
- Coding
- c.2010C>T
- MANE Select
- NM_005932
- Type
- single nucleotide variant
- Location
- chr13:23756579 (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-his670 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown