IFT88 p.Pro799=
c.2397A>C · VCV3676061
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00339%, nfe)
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 1 | GERP -2.3, phastCons 0.99 |
| Overall | ||
| CADD | 7.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00339%
European (non-Finnish) · 40/1,179,838 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00225%
Overall
0.00254%
41/1,613,774 alleles · very rare
exomes 40/1,461,586 · genomes 1/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00339% | 29,496 |
| Admixed American | 0.00167% | 59,992 |
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.Pro799=
- Coding
- c.2397A>C
- MANE Select
- NM_006531
- Type
- single nucleotide variant
- Location
- chr13:20691097 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI 0.09 (gnomAD)
- Structure
- AlphaFold pLDDT 77.20
- Residue 799
- the 'disordered' region
Similar variants
- IFT88 p.Pro799Ser Uncertain significance ★ ⚠ same residue
- IFT88 p.Pro799Thr Uncertain significance ★ ⚠ same residue
- 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
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-pro799 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown