IFT52 p.Leu41=
c.121T>C · rs755929073 · VCV724655
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, 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 2.9 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 15.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,018 alleles
Filtering AF
8.1e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.5e-05%
Overall
0.000317%
5/1,577,658 alleles · ultra-rare
exomes 3/1,425,422 · genomes 2/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,018 |
| European (non-Finnish) | 0.000346% | 288,610 |
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
- IFT52
- Protein
- p.Leu41=
- Coding
- c.121T>C
- MANE Select
- NM_016004
- dbSNP
- rs755929073
- Type
- single nucleotide variant
- Location
- chr20:43596436 (GRCh38)
- Gene constraint
- LOEUF 1.116 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.21
Similar variants
- IFT52 p.Asn35Ser Uncertain significance ★★ ⚠ same type
- IFT52 p.Glu4Asp Uncertain significance ★★ ⚠ same type
- IFT52 p.Gly134Glu Uncertain significance ★★ ⚠ same type
- IFT52 p.Leu164Phe Uncertain significance ★★ ⚠ same type
- IFT52 p.Leu334Arg Uncertain significance ★★ same type
- IFT52 p.Phe95Ser Uncertain significance ★★ ⚠ same type
- IFT52 p.Pro397Ser Uncertain significance ★★ ⚠ same type
- IFT52 p.Val53Met 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/ift52-p-leu41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown