IQCH p.Pro747=
c.2241A>C · VCV3388457
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.05%, 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 -0.43 | GERP -5.5 |
| Overall | ||
| CADD | 8.395 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.05%
African / African-American · 786/75,034 alleles
Filtering AF
0.987%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.963%
Overall
0.0571%
921/1,614,080 alleles · low-frequency
exomes 472/1,461,786 · genomes 449/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.05% | 95 |
| Middle Eastern | 0.115% | 866 |
| Remaining individualsnot grpmax-eligible | 0.0624% | 1,603 |
| Admixed American | 0.035% | 2,858 |
| European (non-Finnish) | 0.00568% | 17,612 |
| South Asian | 0.0011% | 91,058 |
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
- IQCH
- Protein
- p.Pro747=
- Coding
- c.2241A>C
- MANE Select
- NM_001031715
- Type
- single nucleotide variant
- Location
- chr15:67421313 (GRCh38)
- Gene constraint
- LOEUF 0.861 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.09
Similar variants
- IQCH p.Val305= Benign ★★ same type
- IQCH p.Ala539Thr Uncertain significance ★ ⚠ same type
- IQCH p.Ala588Thr Uncertain significance ★ ⚠ same type
- IQCH p.Ala711Val Uncertain significance ★ ⚠ same type
- IQCH p.Ala718Thr Uncertain significance ★ ⚠ same type
- IQCH p.Ala809Gly Uncertain significance ★ ⚠ same type
- IQCH p.Arg177Gln Uncertain significance ★ ⚠ same type
- IQCH p.Arg207Cys 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/iqch-p-pro747 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown