IQSEC2 p.Arg568=
c.1704T>C · rs1569302421 · VCV590010
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000336%, nfe)
Conditions
1
Inborn genetic diseases
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 1.7 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 9.158 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000336%
European (non-Finnish) · 3/893,479 alleles
Filtering AF
8.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.5e-05%
Overall
0.000274%
3/1,095,133 alleles · very rare
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
- IQSEC2
- Protein
- p.Arg568=
- Coding
- c.1704T>C
- MANE Select
- NM_001111125
- dbSNP
- rs1569302421
- Type
- single nucleotide variant
- Location
- chrX:53250872 (GRCh38)
- Structure
- AlphaFold pLDDT 54.46 · 2 PDB
- Residue 568
- the 'disordered' region
Similar variants
- IQSEC2 p.Arg568Cys Likely benign ★ same residue
- IQSEC2 p.Arg568His Likely benign ★ ⚠ same residue
- IQSEC2 p.Arg359His Likely pathogenic ★★ same condition
- IQSEC2 p.Arg531Ter Pathogenic/Likely pathogenic ★★ same condition
- IQSEC2 p.Arg758Ter Pathogenic ★★ same condition
- IQSEC2 c.2582+3G>T Uncertain significance ★★ same condition
- IQSEC2 c.708-3C>T Uncertain significance ★★ same condition
- IQSEC2 p.Arg1090His Uncertain significance ★★ ⚠ same condition
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/iqsec2-p-arg568 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown