IFT81 p.Leu112=
c.334C>T · rs2137296241 · VCV1664616
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00112%, sas)
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 0.6 | GERP 0.92, phastCons 0.19 |
| Overall | ||
| CADD | 8.188 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00112%
South Asian · 1/89,632 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000186%
3/1,608,772 alleles · very rare
exomes 3/1,456,638 · genomes 0/152,134 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00112% | 89,632 |
| European (non-Finnish) | 0.00017% | 589,293 |
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.Leu112=
- Coding
- c.334C>T
- MANE Select
- NM_014055
- dbSNP
- rs2137296241
- Type
- single nucleotide variant
- Location
- chr12:110129035 (GRCh38)
- Gene constraint
- LOEUF 1.054 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.45
- Residue 112
- the 'ch (calponin-homology)-like region' region
Similar variants
- IFT81 p.Leu112Pro Uncertain significance ★ ⚠ same residue
- 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
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-leu112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown