IFT74 p.Thr589=
c.1767C>T · rs539954518 · VCV2987819
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000341%, nfe)
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 0.26 | GERP -1.5, phastCons 0.11 |
| Overall | ||
| CADD | 8.362 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000341%
European (non-Finnish) · 4/1,174,578 alleles
Filtering AF
8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000249%
4/1,604,294 alleles · very rare
exomes 2/1,452,796 · genomes 2/151,498 · joint denominator
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
- IFT74
- Protein
- p.Thr589=
- Coding
- c.1767C>T
- MANE Select
- NM_025103
- dbSNP
- rs539954518
- Type
- single nucleotide variant
- Location
- chr9:27062700 (GRCh38)
- Gene constraint
- LOEUF 1.508 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.21
- Residue 589
- a UniProt-annotated variant site (in jbts40); the 'important for interaction with ift27' region
Similar variants
- IFT74 c.1685-1G>T Pathogenic/Likely pathogenic ★★ same type
- IFT74 p.Gln179Glu Pathogenic/Likely pathogenic ★★ ⚠ same type
- IFT74 p.Glu120Ter Pathogenic/Likely pathogenic ★★ same type
- IFT74 p.Glu285Ter Pathogenic/Likely pathogenic ★★ same type
- IFT74 p.Ala196Val Uncertain significance ★★ ⚠ same type
- IFT74 p.Ala558Val Uncertain significance ★★ ⚠ same type
- IFT74 p.Arg182Gln Uncertain significance ★★ ⚠ same type
- IFT74 p.Arg402Gly 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/ift74-p-thr589 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown