IFT88 p.Ala552=
c.1656C>T · rs778032657 · VCV1668776
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0916%, sas)
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 -0.73 | GERP -3.4, phastCons 0.009 |
| Overall | ||
| CADD | 9.505 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0916%
South Asian · 83/90,570 alleles
Filtering AF
0.0757%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0698%
Overall
0.00547%
88/1,609,640 alleles · ultra-rare
exomes 82/1,457,960 · genomes 6/151,680 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0916% | 1,091 |
| Admixed American | 0.00334% | 29,935 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,278 |
| European (non-Finnish) | 0.00017% | 588,602 |
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
- IFT88
- Protein
- p.Ala552=
- Coding
- c.1656C>T
- MANE Select
- NM_006531
- dbSNP
- rs778032657
- Type
- single nucleotide variant
- Location
- chr13:20641372 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI 0.09 (gnomAD)
- Structure
- AlphaFold pLDDT 77.20
Similar variants
- IFT88 p.Ala327Thr Uncertain significance ★★ ⚠ same type
- IFT88 p.Ala37Gly Uncertain significance ★★ ⚠ same type
- IFT88 p.Ala458Val Uncertain significance ★★ ⚠ same type
- IFT88 p.Ala510Pro Uncertain significance ★★ ⚠ same type
- IFT88 p.Ala546Thr Uncertain significance ★★ ⚠ same type
- IFT88 p.Ala628Ser Uncertain significance ★★ ⚠ same type
- IFT88 p.Arg369His Uncertain significance ★★ ⚠ same type
- IFT88 p.Arg533Trp 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/ift88-p-ala552 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown