IFT172

Chr 2AR

intraflagellar transport 172

Also known as: BBS20, NPHP17, RP71, SLB, SRTD10, osm-1, wim

NCBI Gene: 26160ENSG00000138002UniProt: Q9UG01OMIM: 607386

The protein is required for the maintenance and formation of cilia and plays an indirect role in hedgehog signaling. Mutations cause autosomal recessive ciliopathies including Bardet-Biedl syndrome, retinitis pigmentosa, and short-rib thoracic dysplasia with or without polydactyly. The gene is extremely intolerant to loss-of-function variants (pLI approaching 1), reflecting the critical importance of proper ciliary function for multiple organ systems including skeletal, retinal, and renal development.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.763 OMIM phenotypes
Clinical Summary— IFT172
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Gene-Disease Validity (ClinGen)
ciliopathy · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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ClinVar Variants
54 unique Pathogenic / Likely Pathogenic· 217 VUS of 500 total submissions
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →
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GeneReview available — IFT172
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.76LOEUF
pLI 0.000
Z-score 3.77
OE 0.62 (0.51–0.76)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.19Z-score
OE missense 0.89 (0.85–0.94)
892 obs / 997.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.62 (0.51–0.76)
0≤0.351.4
Missense OE0.89 (0.85–0.94)
0≤0.61.4
Synonymous OE0.92
0≤1.21.6
LoF obs/exp: 71 / 114.6Missense obs/exp: 892 / 997.4Syn Z: 1.27
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveIFT172-related short-rib thoracic dysplasia with or without polydactylyLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6355th %ile
GOF
0.5170th %ile
LOF
0.3452th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

500 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic22
Likely Pathogenic32
VUS217
Likely Benign188
Benign2
Conflicting12
22
Pathogenic
32
Likely Pathogenic
217
VUS
188
Likely Benign
2
Benign
12
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
18
0
4
0
22
Likely Pathogenic
32
0
0
0
32
VUS
3
193
20
1
217
Likely Benign
0
1
83
104
188
Benign
0
0
2
0
2
Conflicting
—12
Total53194109105473

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

IFT172 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 4 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients