HIVEP2 p.Ser573=
c.1719C>T · rs747664894 · VCV3037203
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0274%, sas)
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 -14 | GERP -5.8 |
| Overall | ||
| CADD | 0.115 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0274%
South Asian · 25/91,080 alleles
Filtering AF
0.019%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0163%
Overall
0.00366%
59/1,614,092 alleles · ultra-rare
exomes 54/1,461,872 · genomes 5/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0274% | 3,643 |
| African / African-American | 0.008% | 12,500 |
| Finnishnot grpmax-eligible | 0.00625% | 16,001 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,837 |
| Admixed American | 0.00333% | 30,014 |
| European (non-Finnish) | 0.00161% | 62,106 |
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.Ser573=
- Coding
- c.1719C>T
- MANE Select
- NM_006734
- dbSNP
- rs747664894
- Type
- single nucleotide variant
- Location
- chr6:142773020 (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-ser573 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown