HIVEP2 p.His1237=
c.3711C>T · VCV3646884
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
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 -0.063 | GERP -2.1, phastCons 0.031 |
| Overall | ||
| CADD | 2.506 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Overall
0.000124%
2/1,614,206 alleles · ultra-rare
exomes 2/1,461,874 · genomes 0/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| European (non-Finnish) | 8.47e-05% | 1,180,043 |
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.His1237=
- Coding
- c.3711C>T
- MANE Select
- NM_006734
- Type
- single nucleotide variant
- Location
- chr6:142771028 (GRCh38)
- Gene constraint
- LOEUF 0.114 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.43
Similar variants
- 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
- HIVEP2 p.Arg1497Gln Uncertain significance ★★ ⚠ same type
- HIVEP2 p.Arg1794Cys 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-his1237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown