IQCE p.Ala293=
c.879C>T · rs61736928 · VCV783485
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.11%, 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 -1.6 | GERP -3.1 |
| Overall | ||
| CADD | 1.458 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.11%
African / African-American · 2,335/75,034 alleles
Filtering AF
3.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.96%
Overall
0.162%
2,621/1,614,020 alleles · low-frequency
exomes 1,277/1,461,712 · genomes 1,344/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.11% | 32 |
| Admixed American | 0.177% | 566 |
| Remaining individualsnot grpmax-eligible | 0.162% | 619 |
| Middle Eastern | 0.0825% | 1,212 |
| European (non-Finnish) | 0.00585% | 17,101 |
| South Asian | 0.00549% | 18,216 |
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.Ala293=
- Coding
- c.879C>T
- MANE Select
- NM_152558
- dbSNP
- rs61736928
- Type
- single nucleotide variant
- Location
- chr7:2586262 (GRCh38)
- Gene constraint
- LOEUF 1.442 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.36
Similar variants
- 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
- IQCE p.Tyr255Ter Pathogenic ★ same type
- IQCE c.1440+1G>T 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-ala293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown