IQCE p.Ala545=
c.1635G>A · rs371441568 · VCV3035295
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0231%, nfe)
Conditions
1
IQCE-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.29 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.7 | GERP -2.2 |
| Overall | ||
| CADD | 1.937 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0231%
European (non-Finnish) · 272/1,179,060 alleles
Filtering AF
0.0208%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0199%
Overall
0.0181%
292/1,612,560 alleles · ultra-rare
exomes 280/1,460,410 · genomes 12/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0231% | 4,335 |
| African / African-American | 0.0134% | 7,488 |
| Admixed American | 0.01% | 9,998 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,609 |
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.Ala545=
- Coding
- c.1635G>A
- MANE Select
- NM_152558
- dbSNP
- rs371441568
- Type
- single nucleotide variant
- Location
- chr7:2604883 (GRCh38)
- Gene constraint
- LOEUF 1.442 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.36
- Residue 545
- the iq 1 domain
Disease context
IQCE-related disorder
Similar variants
- IQCE p.Arg394Ter Likely pathogenic same condition
- IQCE p.Lys289Ter Uncertain significance same condition
- IQCE c.1969+146G>A Benign same condition
- IQCE c.-2C>T Likely benign same condition
- IQCE p.Ala208= Likely benign same condition
- IQCE p.Arg341Lys Benign same condition
- IQCE p.Asp230= Likely benign same condition
- IQCE p.Leu393= Likely benign 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/iqce-p-ala545 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown