IFT74 p.Ser598=
c.1794C>T · rs201682450 · VCV1594050
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0336%, mid)
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 0.4 | GERP -1.8, phastCons 0.14 |
| Overall | ||
| CADD | 8.641 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0336%
Middle Eastern · 2/5,958 alleles
Filtering AF
0.0268%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0258%
Overall
0.0243%
379/1,560,626 alleles · ultra-rare
exomes 351/1,409,422 · genomes 28/151,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0336% | 2,979 |
| European (non-Finnish) | 0.0294% | 3,399 |
| Remaining individualsnot grpmax-eligible | 0.0264% | 3,791 |
| South Asian | 0.0161% | 6,225 |
| African / African-American | 0.0109% | 9,148 |
| Admixed American | 0.00522% | 19,172 |
| East Asian | 0.00228% | 43,854 |
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.Ser598=
- Coding
- c.1794C>T
- MANE Select
- NM_025103
- dbSNP
- rs201682450
- Type
- single nucleotide variant
- Location
- chr9:27062727 (GRCh38)
- Gene constraint
- LOEUF 1.508 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.21
- Residue 598
- 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-ser598 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown