IFT172 p.Pro197=
c.591G>A · rs747654101 · VCV1110946
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
Conditions
3
inherited retinal dystrophy
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 -13 | GERP -5 |
| Overall | ||
| CADD | 0.611 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,880 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000892%
Overall
0.0011%
16/1,459,772 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,440 |
| South Asian | 0.0044% | 22,730 |
| African / African-American | 0.004% | 24,987 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,342 |
| European (non-Finnish) | 0.000509% | 196,639 |
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.Pro197=
- Coding
- c.591G>A
- MANE Select
- NM_015662
- dbSNP
- rs747654101
- Type
- single nucleotide variant
- Location
- chr2:27481240 (GRCh38)
- Gene constraint
- LOEUF 0.745 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.98 · 1 PDB
Similar variants
- IFT172 p.Pro197Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- IFT172 p.Pro197Ser Uncertain significance ★ ⚠ same residue
- IFT172 c.1411+2T>C Likely pathogenic ★★ same condition
- IFT172 c.1525-1G>A Pathogenic/Likely pathogenic ★★ same condition
- IFT172 c.184-2A>C Likely pathogenic ★★ same condition
- IFT172 c.2443-1G>C Likely pathogenic ★★ same condition
- IFT172 c.2976-2A>T Likely pathogenic ★★ same condition
- IFT172 c.3111+1G>T 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-pro197 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown