IFT122 p.Val615=
c.1845G>A · VCV3605472
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000126%)
Conditions
1
cranioectodermal dysplasia 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.48 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.23 | gain · loss 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 2.3 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 14.89 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000126%
Overall
0.000126%
2/1,593,540 alleles · very rare
exomes 1/1,441,340 · genomes 1/152,200 · joint denominator
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.Val615=
- Coding
- c.1845G>A
- MANE Select
- NM_052989
- Type
- single nucleotide variant
- Location
- chr3:129483676 (GRCh38)
- Gene constraint
- LOEUF 0.811 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.91 · 5 PDB
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-val615 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown