IFT88 p.Cys401=
c.1203C>T · rs763771455 · VCV1438114
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0171%, mid)
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 0.86 | GERP -4.2, phastCons 1 |
| Overall | ||
| CADD | 5.765 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0171%
Middle Eastern · 1/5,848 alleles
Filtering AF
0.00733%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00558%
Overall
0.0022%
35/1,593,454 alleles · ultra-rare
exomes 25/1,441,518 · genomes 10/151,936 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0171% | 5,848 |
| African / African-American | 0.0136% | 7,377 |
| Admixed American | 0.00887% | 11,280 |
| South Asian | 0.00341% | 29,315 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00341% | 29,324 |
| Remaining individualsnot grpmax-eligible | 0.00324% | 30,847 |
| European (non-Finnish) | 0.00111% | 89,970 |
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.Cys401=
- Coding
- c.1203C>T
- MANE Select
- NM_006531
- dbSNP
- rs763771455
- Type
- single nucleotide variant
- Location
- chr13:20625753 (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-cys401 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown