HIVEP2 p.Pro86=
c.258G>A · rs188298782 · VCV716952
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.605%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.2 | GERP -5 |
| Overall | ||
| CADD | 7.057 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.605%
African / African-American · 454/74,982 alleles
Filtering AF
0.559%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.541%
Overall
0.0338%
545/1,614,020 alleles · rare
exomes 284/1,461,890 · genomes 261/152,130 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.605% | 165 |
| Middle Eastern | 0.0825% | 1,212 |
| Remaining individualsnot grpmax-eligible | 0.064% | 1,563 |
| Admixed American | 0.0467% | 2,143 |
| East Asian | 0.00446% | 22,429 |
| South Asian | 0.00439% | 22,769 |
| European (non-Finnish) | 0.00102% | 98,333 |
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
- HIVEP2
- Protein
- p.Pro86=
- Coding
- c.258G>A
- MANE Select
- NM_006734
- dbSNP
- rs188298782
- Type
- single nucleotide variant
- Location
- chr6:142774481 (GRCh38)
- Gene constraint
- LOEUF 0.114 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.43
- Residue 86
- the 'disordered' region
Similar variants
- HIVEP2 p.Pro86Leu Likely benign ★ same residue
- HIVEP2 p.Pro86Ser Likely benign ★ same residue
- HIVEP2 p.Arg1979Ter Pathogenic ★★ same type
- HIVEP2 p.Arg2223Ter Pathogenic ★★ same type
- HIVEP2 p.Arg943Ter Pathogenic ★★ same type
- HIVEP2 p.Gln1138Ter Pathogenic ★★ same type
- HIVEP2 p.Ala1501Asp Uncertain significance ★★ same type
- HIVEP2 p.Ala437Ser 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/hivep2-p-pro86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown