IFT52 p.Ala13=
c.39C>T · VCV4761200
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, 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 -1.3 | GERP -3.8 |
| Overall | ||
| CADD | 5.896 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
African / African-American · 5/74,860 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00162%
Overall
0.000992%
16/1,612,542 alleles · very rare
exomes 8/1,460,464 · genomes 8/152,078 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00668% | 14,972 |
| European (non-Finnish) | 0.000933% | 107,161 |
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.Ala13=
- Coding
- c.39C>T
- MANE Select
- NM_016004
- Type
- single nucleotide variant
- Location
- chr20:43594737 (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-ala13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown