IFT88 p.Arg369=
c.1107T>C · rs143814635 · VCV1585951
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.022%, nfe)
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 2.8 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 9.84 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.022%
European (non-Finnish) · 218/990,860 alleles
Filtering AF
0.0196%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0186%
Overall
0.0166%
232/1,394,112 alleles · ultra-rare
exomes 218/1,241,842 · genomes 14/152,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.022% | 4,545 |
| Remaining individualsnot grpmax-eligible | 0.0146% | 6,857 |
| Admixed American | 0.00874% | 11,445 |
| African / African-American | 0.00142% | 70,432 |
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.Arg369=
- Coding
- c.1107T>C
- MANE Select
- NM_006531
- dbSNP
- rs143814635
- Type
- single nucleotide variant
- Location
- chr13:20605100 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI 0.09 (gnomAD)
- Structure
- AlphaFold pLDDT 77.20
Similar variants
- IFT88 p.Arg369His Uncertain significance ★★ ⚠ same residue
- IFT88 p.Arg369Cys 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-arg369 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown