HIVEP2 p.Ser41=
c.123T>C · VCV4780389
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
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 1.4 | GERP -0.94, phastCons 1 |
| Overall | ||
| CADD | 6.844 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,002 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000186%
3/1,614,064 alleles · very rare
exomes 2/1,461,894 · genomes 1/152,170 · joint denominator
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.Ser41=
- Coding
- c.123T>C
- MANE Select
- NM_006734
- Type
- single nucleotide variant
- Location
- chr6:142774616 (GRCh38)
- Gene constraint
- LOEUF 0.114 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.43
- Residue 41
- the 'disordered' region
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-ser41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown