IFT81 p.Arg115=
c.345A>G · rs757397458 · VCV1541298
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.027%, sas)
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 | GERP -0.68, phastCons 1 |
| Overall | ||
| CADD | 9.509 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.027%
South Asian · 24/88,942 alleles
Filtering AF
0.0186%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0158%
Overall
0.00261%
42/1,606,412 alleles · ultra-rare
exomes 41/1,454,250 · genomes 1/152,162 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.027% | 3,706 |
| Remaining individualsnot grpmax-eligible | 0.00482% | 20,740 |
| European (non-Finnish) | 0.00127% | 78,540 |
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
- IFT81
- Protein
- p.Arg115=
- Coding
- c.345A>G
- MANE Select
- NM_014055
- dbSNP
- rs757397458
- Type
- single nucleotide variant
- Location
- chr12:110129046 (GRCh38)
- Gene constraint
- LOEUF 1.054 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.45
- Residue 115
- the 'ch (calponin-homology)-like region' region
Similar variants
- IFT81 c.1717-2A>G Pathogenic/Likely pathogenic ★★ same type
- IFT81 c.249-1G>A Pathogenic/Likely pathogenic ★★ same type
- IFT81 p.Arg213Ter Pathogenic/Likely pathogenic ★★ same type
- IFT81 p.Arg399Ter Pathogenic/Likely pathogenic ★★ same type
- IFT81 p.Arg481Ter Pathogenic/Likely pathogenic ★★ same type
- IFT81 p.Arg512Ter Pathogenic/Likely pathogenic ★★ same type
- IFT81 p.Arg64Ter Pathogenic ★★ same type
- IFT81 p.Leu122Ter Pathogenic/Likely pathogenic ★★ 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/ift81-p-arg115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown