IQCE p.Pro51=
c.153G>A · VCV4895041
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.03%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.28 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.8 | GERP -2.9 |
| Overall | ||
| CADD | 2.823 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.03%
African / African-American · 771/75,030 alleles
Filtering AF
0.967%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.943%
Overall
0.0621%
998/1,606,184 alleles · low-frequency
exomes 577/1,453,926 · genomes 421/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.03% | 97 |
| Middle Eastern | 0.346% | 289 |
| Remaining individualsnot grpmax-eligible | 0.109% | 919 |
| Admixed American | 0.1% | 1,000 |
| European (non-Finnish) | 0.00653% | 15,324 |
| South Asian | 0.0011% | 91,076 |
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.Pro51=
- Coding
- c.153G>A
- MANE Select
- NM_152558
- Type
- single nucleotide variant
- Location
- chr7:2571548 (GRCh38)
- Gene constraint
- LOEUF 1.442 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.36
- Residue 51
- the 'disordered' region
Similar variants
- IQCE p.Pro51Leu Uncertain significance ★ ⚠ 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
- IQCE p.Tyr255Ter 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-pro51 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown