IQCE p.Arg511=
c.1533C>T · rs114555800 · VCV709084
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.444%, 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 -1.8 | GERP -3 |
| Overall | ||
| CADD | 1.755 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.444%
African / African-American · 332/74,846 alleles
Filtering AF
0.404%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.389%
Overall
0.022%
354/1,610,534 alleles · rare
exomes 176/1,458,182 · genomes 178/152,352 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.444% | 225 |
| Middle Eastern | 0.0331% | 3,020 |
| Admixed American | 0.0168% | 5,937 |
| Remaining individualsnot grpmax-eligible | 0.0161% | 6,230 |
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
- IQCE
- Protein
- p.Arg511=
- Coding
- c.1533C>T
- MANE Select
- NM_152558
- dbSNP
- rs114555800
- Type
- single nucleotide variant
- Location
- chr7:2598557 (GRCh38)
- Gene constraint
- LOEUF 1.442 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.36
- Residue 511
- the 'disordered' region
Similar variants
- IQCE p.Arg511His Uncertain significance ★ ⚠ same residue
- IQCE p.Arg511Cys Benign ★ same residue
- IQCE p.Lys538Arg Uncertain significance ★★ ⚠ same type
- IQCE p.Asp645= Benign/Likely benign ★★ same type
- IQCE p.Leu277= Benign/Likely benign ★★ same type
- IQCE p.Pro586Ser Likely benign ★★ same type
- IQCE p.Met1Ile Likely pathogenic ★ same type
- IQCE p.Trp498Ter 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/iqce-p-arg511 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown