IK p.Phe9=
c.27C>T · rs535506489 · VCV724585
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.576%, sas)
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 0.44 | GERP -2, phastCons 0.99 |
| Overall | ||
| CADD | 13.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.576%
South Asian · 525/91,082 alleles
Filtering AF
0.536%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.519%
Overall
0.0343%
554/1,614,000 alleles · rare
exomes 508/1,461,672 · genomes 46/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.576% | 173 |
| Remaining individualsnot grpmax-eligible | 0.0416% | 2,403 |
| East Asian | 0.00223% | 44,880 |
| European (non-Finnish) | 0.00017% | 589,932 |
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
- IK
- Protein
- p.Phe9=
- Coding
- c.27C>T
- MANE Select
- NM_006083
- dbSNP
- rs535506489
- Type
- single nucleotide variant
- Location
- chr5:140648481 (GRCh38)
- Gene constraint
- LOEUF 0.771 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.95 · 5 PDB
- Residue 9
- the 'disordered' region
Similar variants
- IK p.Ala14Asp Uncertain significance ★ ⚠ same type
- IK p.Ala446Ser Uncertain significance ★ same type
- IK p.Arg214Cys Uncertain significance ★ ⚠ same type
- IK p.Arg214His Uncertain significance ★ ⚠ same type
- IK p.Arg334Gln Uncertain significance ★ ⚠ same type
- IK p.Arg342Gln Uncertain significance ★ ⚠ same type
- IK p.Arg342Trp Uncertain significance ★ ⚠ same type
- IK p.Arg344Gln 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/ik-p-phe9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown