IFT27 p.Ala30=
c.90C>T · rs376757393 · VCV1432659
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.132%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.39 | GERP -1.2, phastCons 0.97 |
| Overall | ||
| CADD | 13.35 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.132%
Middle Eastern · 8/6,060 alleles
Filtering AF
0.0657%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0479%
Overall
0.00409%
66/1,614,166 alleles · rare
exomes 60/1,461,862 · genomes 6/152,304 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.132% | 758 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,814 |
| African / African-American | 0.00666% | 15,007 |
| Admixed American | 0.005% | 20,009 |
| European (non-Finnish) | 0.00331% | 30,257 |
| South Asian | 0.00329% | 30,361 |
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
- IFT27
- Protein
- p.Ala30=
- Coding
- c.90C>T
- MANE Select
- NM_001177701
- dbSNP
- rs376757393
- Type
- single nucleotide variant
- Location
- chr22:36767807 (GRCh38)
- Gene constraint
- LOEUF 1.078 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 92.65
Similar variants
- IFT27 p.Tyr36Cys Pathogenic ★★ same type
- IFT27 c.114+5G>T Uncertain significance ★★ same type
- IFT27 p.Arg26Cys Uncertain significance ★★ ⚠ same type
- IFT27 p.Arg26His Uncertain significance ★★ ⚠ same type
- IFT27 p.Leu44Phe Uncertain significance ★★ same type
- IFT27 p.Lys3Gln Uncertain significance ★★ ⚠ same type
- IFT27 c.114+8G>A Likely benign ★★ same type
- IFT27 c.174+17C>T Likely benign ★★ 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/ift27-p-ala30 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown