IFT52 p.Val115=
c.345G>A · rs773423798 · VCV3004213
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00667%, amr)
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 5 | phastCons 1 |
| Overall | ||
| CADD | 7.504 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
Admixed American · 4/59,968 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.000623%
10/1,604,946 alleles · very rare
exomes 9/1,452,830 · genomes 1/152,116 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00667% | 14,992 |
| East Asian | 0.00223% | 44,846 |
| European (non-Finnish) | 0.000427% | 234,368 |
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.Val115=
- Coding
- c.345G>A
- MANE Select
- NM_016004
- dbSNP
- rs773423798
- Type
- single nucleotide variant
- Location
- chr20:43604190 (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-val115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown