IFT27 p.Ile9=
c.27C>T · rs183375553 · VCV1921131
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0602%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.9 | GERP 0.59, phastCons 1 |
| Overall | ||
| CADD | 14.99 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0602%
East Asian · 27/44,880 alleles
Filtering AF
0.0424%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0365%
Overall
0.00167%
27/1,614,152 alleles · ultra-rare
exomes 25/1,461,858 · genomes 2/152,294 · joint denominator
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
- IFT27
- Protein
- p.Ile9=
- Coding
- c.27C>T
- MANE Select
- NM_001177701
- dbSNP
- rs183375553
- Type
- single nucleotide variant
- Location
- chr22:36775681 (GRCh38)
- Gene constraint
- LOEUF 1.078 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 92.65
Similar variants
- IFT27 p.Tyr36Cys Pathogenic ★★ same type
- IFT27 c.114+5G>T Uncertain significance ★★ same type
- IFT27 p.Arg26Cys Uncertain significance ★★ ⚠ same type
- IFT27 p.Arg26His Uncertain significance ★★ ⚠ same type
- IFT27 p.Leu44Phe Uncertain significance ★★ same type
- IFT27 p.Lys3Gln Uncertain significance ★★ ⚠ same type
- IFT27 c.114+8G>A Likely benign ★★ same type
- IFT27 c.174+17C>T Likely benign ★★ 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/ift27-p-ile9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown