IFT172 p.Pro200=
c.600C>T · VCV3357114
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00401%, afr)
Conditions
1
IFT172-related disorder
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 -0.14 | GERP -1.7, phastCons 0.092 |
| Overall | ||
| CADD | 6.721 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00401%
African / African-American · 3/74,844 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000248%
4/1,611,990 alleles · very rare
exomes 2/1,459,864 · genomes 2/152,126 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00401% | 24,948 |
| South Asian | 0.0011% | 90,920 |
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
- IFT172
- Protein
- p.Pro200=
- Coding
- c.600C>T
- MANE Select
- NM_015662
- Type
- single nucleotide variant
- Location
- chr2:27481231 (GRCh38)
- Gene constraint
- LOEUF 0.745 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.98 · 1 PDB
Disease context
IFT172-related disorder
Similar variants
- IFT172 p.Pro200Arg Uncertain significance ★ ⚠ same residue
- IFT172 c.1525-1G>A Pathogenic/Likely pathogenic ★★ same condition
- IFT172 c.184-2A>C Likely pathogenic ★★ same condition
- IFT172 c.786-2A>G Likely pathogenic ★★ same condition
- IFT172 p.Arg346Ter Pathogenic/Likely pathogenic ★★ same condition
- IFT172 p.Arg38Ter Pathogenic/Likely pathogenic ★★ same condition
- IFT172 p.Arg685Ter Pathogenic/Likely pathogenic ★★ same condition
- IFT172 p.Arg789Ter Pathogenic/Likely 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/ift172-p-pro200 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown