IFT52 p.Ala182=
c.546G>C · rs766004382 · VCV2970280
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, mid)
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 -1.3 | GERP -1.3, phastCons 0.002 |
| Overall | ||
| CADD | 6.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,062 alleles
Filtering AF
0.0172%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0146%
Overall
0.00161%
26/1,613,910 alleles · ultra-rare
exomes 24/1,461,654 · genomes 2/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,031 |
| South Asian | 0.0253% | 3,960 |
| European (non-Finnish) | 8.48e-05% | 1,179,842 |
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.Ala182=
- Coding
- c.546G>C
- MANE Select
- NM_016004
- dbSNP
- rs766004382
- Type
- single nucleotide variant
- Location
- chr20:43613910 (GRCh38)
- Gene constraint
- LOEUF 1.116 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.21
Similar variants
- IFT52 p.Ala182Val Uncertain significance ★ ⚠ same residue
- IFT52 p.Ala182fs 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
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-ala182 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown