IQCE p.Asp645=
c.1935C>T · rs150273271 · VCV718617
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.7%, eas)
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 -2.5 | GERP -7.6 |
| Overall | ||
| CADD | 0.257 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.7%
East Asian · 764/44,836 alleles
Filtering AF
1.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.56%
Overall
0.0637%
1,028/1,613,654 alleles · low-frequency
exomes 899/1,461,364 · genomes 129/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.7% | 59 |
| South Asian | 0.101% | 989 |
| Remaining individualsnot grpmax-eligible | 0.072% | 1,388 |
| Middle Eastern | 0.033% | 3,028 |
| Admixed American | 0.0217% | 4,615 |
| African / African-American | 0.0173% | 5,769 |
| European (non-Finnish) | 0.00814% | 12,289 |
| Finnishnot grpmax-eligible | 0.00469% | 21,341 |
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.Asp645=
- Coding
- c.1935C>T
- MANE Select
- NM_152558
- dbSNP
- rs150273271
- Type
- single nucleotide variant
- Location
- chr7:2607193 (GRCh38)
- Gene constraint
- LOEUF 1.442 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.36
- Residue 645
- the 'disordered' region
Similar variants
- IQCE p.Lys538Arg Uncertain significance ★★ ⚠ 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
- IQCE p.Tyr255Ter Pathogenic ★ same type
- IQCE c.1440+1G>T Uncertain significance ★ same type
- IQCE c.825-2A>G 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/iqce-p-asp645 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown