IQSEC2 p.Gly485=
c.1455G>C · rs2519811030 · VCV2660604
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.49 | GERP 0.93, phastCons 0.98 |
| Overall | ||
| CADD | 5.931 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- IQSEC2
- Protein
- p.Gly485=
- Coding
- c.1455G>C
- MANE Select
- NM_001111125
- dbSNP
- rs2519811030
- Type
- single nucleotide variant
- Location
- chrX:53251121 (GRCh38)
- Structure
- AlphaFold pLDDT 54.46 · 2 PDB
- Residue 485
- the 'disordered' region
Similar variants
- IQSEC2 p.Gly485Glu Benign ★ same residue
- IQSEC2 c.2459+21C>T Pathogenic ★★ same type
- IQSEC2 c.2889+1G>A Pathogenic ★★ same type
- IQSEC2 p.Ala836Val Pathogenic/Likely pathogenic ★★ same type
- IQSEC2 p.Arg1055Ter Pathogenic ★★ same type
- IQSEC2 p.Arg1145Ter Pathogenic ★★ same type
- IQSEC2 p.Arg359His Likely pathogenic ★★ same type
- IQSEC2 p.Arg531Ter Pathogenic/Likely pathogenic ★★ 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/iqsec2-p-gly485 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown