IFT81 p.Ser2=
c.6T>C · rs1412802929 · VCV1660120
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0319%, eas)
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 2.9 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 10.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0319%
East Asian · 14/43,932 alleles
Filtering AF
0.0192%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0154%
Overall
0.00102%
16/1,574,610 alleles · ultra-rare
exomes 12/1,422,422 · genomes 4/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0319% | 3,138 |
| Remaining individualsnot grpmax-eligible | 0.0033% | 30,347 |
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.Ser2=
- Coding
- c.6T>C
- MANE Select
- NM_014055
- dbSNP
- rs1412802929
- Type
- single nucleotide variant
- Location
- chr12:110127386 (GRCh38)
- Gene constraint
- LOEUF 1.054 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.45
- Residue 2
- the 'ch (calponin-homology)-like region' region; a modified residue (n-acetylserine)
Similar variants
- IFT81 p.Ser2Gly 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-ser2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown