IFT74 p.Leu101=
c.303T>A · rs760997513 · VCV1636603
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.251%, sas)
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 0.66 | GERP 0.036, phastCons 1 |
| Overall | ||
| CADD | 9.627 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.251%
South Asian · 226/90,176 alleles
Filtering AF
0.224%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.213%
Overall
0.0193%
306/1,587,608 alleles · rare
exomes 289/1,435,306 · genomes 17/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.251% | 399 |
| Middle Eastern | 0.0836% | 1,196 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0272% | 3,671 |
| Remaining individualsnot grpmax-eligible | 0.0114% | 8,798 |
| European (non-Finnish) | 0.00484% | 20,659 |
| African / African-American | 0.00403% | 24,799 |
| Admixed American | 0.00168% | 59,676 |
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.Leu101=
- Coding
- c.303T>A
- MANE Select
- NM_025103
- dbSNP
- rs760997513
- Type
- single nucleotide variant
- Location
- chr9:26980617 (GRCh38)
- Gene constraint
- LOEUF 1.508 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.21
- Residue 101
- a UniProt-annotated variant site (in jbts40)
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-leu101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown