IFT52 p.Arg33=
c.97C>A · VCV3627656
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, afr)
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 4.9 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 13.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
African / African-American · 10/74,610 alleles
Filtering AF
0.00726%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00552%
Overall
0.000753%
12/1,594,190 alleles · ultra-rare
exomes 5/1,441,958 · genomes 7/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0134% | 7,461 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 61,936 |
| South Asian | 0.0011% | 90,630 |
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.Arg33=
- Coding
- c.97C>A
- MANE Select
- NM_016004
- Type
- single nucleotide variant
- Location
- chr20:43594795 (GRCh38)
- Gene constraint
- LOEUF 1.116 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.21
Similar variants
- IFT52 p.Arg33Trp Uncertain significance ★ ⚠ same residue
- 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
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-arg33 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown