IFT122 p.Ala653=
c.1959G>A · rs753552899 · VCV2054987
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.028%, afr)
Conditions
1
cranioectodermal dysplasia 1
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 -1.2 | GERP -3.8, phastCons 0.001 |
| Overall | ||
| CADD | 7.087 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.028%
African / African-American · 21/75,044 alleles
Filtering AF
0.0187%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0157%
Overall
0.00335%
54/1,614,188 alleles · ultra-rare
exomes 40/1,461,882 · genomes 14/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.028% | 3,574 |
| South Asian | 0.0176% | 5,692 |
| Middle Eastern | 0.0165% | 6,062 |
| East Asian | 0.00891% | 11,222 |
| Admixed American | 0.00167% | 60,034 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
| European (non-Finnish) | 0.000847% | 118,003 |
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
- IFT122
- Protein
- p.Ala653=
- Coding
- c.1959G>A
- MANE Select
- NM_052989
- dbSNP
- rs753552899
- Type
- single nucleotide variant
- Location
- chr3:129488364 (GRCh38)
- Gene constraint
- LOEUF 0.811 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.91 · 5 PDB
- Residue 653
- an α-helix
Similar variants
- IFT122 c.1148-1G>C Pathogenic/Likely pathogenic ★★ same condition
- IFT122 c.272+1G>A Likely pathogenic ★★ same condition
- IFT122 c.273-257C>A Pathogenic/Likely pathogenic ★★ same condition
- IFT122 c.3265+1G>A Pathogenic/Likely pathogenic ★★ same condition
- IFT122 p.Arg1185Ter Pathogenic/Likely pathogenic ★★ same condition
- IFT122 p.Arg189Ter Pathogenic/Likely pathogenic ★★ same condition
- IFT122 p.Arg673Ter Pathogenic/Likely pathogenic ★★ same condition
- IFT122 p.Gln1005Ter Pathogenic ★★ same condition
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/ift122-p-ala653 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown