HIVEP2 p.Val601=
c.1803A>T · rs371456694 · VCV2786205
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00401%, afr)
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 -2.9 | GERP -5.7 |
| Overall | ||
| CADD | 0.163 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00401%
African / African-American · 3/74,904 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.00031%
5/1,614,026 alleles · very rare
exomes 2/1,461,864 · genomes 3/152,162 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00401% | 24,968 |
| South Asian | 0.0022% | 45,541 |
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.Val601=
- Coding
- c.1803A>T
- MANE Select
- NM_006734
- dbSNP
- rs371456694
- Type
- single nucleotide variant
- Location
- chr6:142772936 (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-val601 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown