IFT81 p.Lys264=
c.792G>A · rs540684366 · VCV734183
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.267%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.26 | acceptor loss, 10 bp away · masked 0 · deltas |
|---|---|---|
| Pangolin | Δ0.21 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 2.7, phastCons 1 |
| Overall | ||
| CADD | 3.589 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.267%
African / African-American · 175/65,476 alleles
Filtering AF
0.235%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.222%
Overall
0.0182%
242/1,330,584 alleles · rare
exomes 118/1,178,436 · genomes 124/152,148 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.267% | 374 |
| Middle Eastern | 0.0265% | 3,776 |
| Remaining individualsnot grpmax-eligible | 0.0235% | 4,248 |
| Admixed American | 0.0179% | 5,582 |
| European (non-Finnish) | 0.00482% | 20,729 |
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.Lys264=
- Coding
- c.792G>A
- MANE Select
- NM_014055
- dbSNP
- rs540684366
- Type
- single nucleotide variant
- Location
- chr12:110143392 (GRCh38)
- Gene constraint
- LOEUF 1.054 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.45
- Residue 264
- a UniProt-annotated variant site (in srtd19)
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-lys264 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown