IFT74 p.Thr84=
c.252G>A · rs374010822 · VCV720134
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0294%, afr)
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 7.1 | GERP -0.2, phastCons 1 |
| Overall | ||
| CADD | 13.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0294%
African / African-American · 22/74,858 alleles
Filtering AF
0.0199%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0168%
Overall
0.00806%
130/1,612,598 alleles · ultra-rare
exomes 120/1,460,460 · genomes 10/152,138 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0294% | 3,403 |
| European (non-Finnish) | 0.00831% | 12,037 |
| Remaining individualsnot grpmax-eligible | 0.00801% | 12,484 |
| Admixed American | 0.00672% | 14,877 |
| East Asian | 0.00223% | 44,776 |
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.Thr84=
- Coding
- c.252G>A
- MANE Select
- NM_025103
- dbSNP
- rs374010822
- Type
- single nucleotide variant
- Location
- chr9:26978259 (GRCh38)
- Gene constraint
- LOEUF 1.508 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.21
- Residue 84
- the 'basic region' region; a UniProt-annotated variant site (in jbts40)
Similar variants
- IFT74 p.Thr84Arg Uncertain significance ★ ⚠ same residue
- IFT74 p.Thr84Met Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-thr84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown