IFT88 p.Ser746=
c.2238C>T · rs202072254 · VCV1552904
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.69%, 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 1 | GERP 0.38, phastCons 1 |
| Overall | ||
| CADD | 9.968 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.69%
South Asian · 1,538/90,972 alleles
Filtering AF
1.62%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.59%
Overall
0.132%
2,125/1,613,150 alleles · low-frequency
exomes 2,023/1,460,968 · genomes 102/152,182 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.69% | 59 |
| East Asian | 0.397% | 252 |
| Remaining individualsnot grpmax-eligible | 0.202% | 496 |
| Middle Eastern | 0.0495% | 2,020 |
| European (non-Finnish) | 0.0225% | 4,451 |
| Finnishnot grpmax-eligible | 0.0141% | 7,111 |
| African / African-American | 0.00667% | 14,994 |
| Admixed American | 0.00167% | 59,936 |
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.Ser746=
- Coding
- c.2238C>T
- MANE Select
- NM_006531
- dbSNP
- rs202072254
- Type
- single nucleotide variant
- Location
- chr13:20671035 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI 0.09 (gnomAD)
- Structure
- AlphaFold pLDDT 77.20
- Residue 746
- the 'disordered' region
Similar variants
- IFT88 p.Ser746Thr 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
- IFT88 p.Arg369His 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-ser746 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown