IFT20

Chr 17

intraflagellar transport 20

NCBI Gene: 90410ENSG00000109083UniProt: Q8IY31

This gene encodes a intraflagellar transport protein important for intracellular transport. The encoded protein forms part of a complex involved in trafficking of proteins from the Golgi body, including recycling of immune signalling components (Finetti et al., PubMed: 19855387). This gene is part of a complex set of sense-antisense loci that may be co-regulated. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. A pseudogene of this gene is located on the long arm of chromosome 14.[provided by RefSeq, Jun 2012]

0
Active trials
29
ClinVar variants
6
Pathogenic / LP
0.1
Missense Z
0.85
LOEUF
5
Pubs (2 yr)
Clinical Summary— IFT20
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.33) despite low pLI — interpret in context.
📋
ClinVar Variants
6 Pathogenic / Likely Pathogenic· 21 VUS of 29 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.85LOEUF
pLI 0.103
Z-score 1.87
OE 0.33 (0.15–0.85)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.12Z-score
OE missense 0.96 (0.80–1.17)
77 obs / 79.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.33 (0.15–0.85)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.96 (0.80–1.17)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.90
0≤1.21.6
LoF obs/exp: 3 / 9.1Missense obs/exp: 77 / 79.9Syn Z: 0.39

ClinVar Variant Classifications

29 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic5
Likely Pathogenic1
VUS21
Likely Benign1
Benign1
5
Pathogenic
1
Likely Pathogenic
21
VUS
1
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
5
0
5
Likely Pathogenic
0
0
1
0
1
VUS
0
18
3
0
21
Likely Benign
0
1
0
0
1
Benign
0
0
1
0
1
Total01910029

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

View in ClinVar →

Protein Context — Lollipop Plot

IFT20 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
DLG1 functions upstream of SDCCAG3 and IFT20 to control ciliary targeting of polycystin-2.
Rezi CK et al.·EMBO Rep
2024
Deletion of IFT20 exclusively in the RPE ablates primary cilia and leads to retinal degeneration.
Kretschmer V et al.·PLoS Biol
2023
Trisomy 21 Represses Cilia Formation and Function.
Galati DF et al.·Dev Cell
2018
A mutation in VPS15 (PIK3R4) causes a ciliopathy and affects IFT20 release from the cis-Golgi.
Stoetzel C et al.·Nat Commun
2016
KIF3B gene silent variant leading to sperm morphology and motility defects and male infertility†.
Heydari R et al.·Biol Reprod
2022
Biallelic mutations in CFAP54 cause male infertility with severe MMAF and NOA.
Tian S et al.·J Med Genet
2023
Homozygous mutations in CCDC34 cause male infertility with oligoasthenoteratozoospermia in humans and mice.
Cong J et al.·J Med Genet
2022
New Mutations in DNHD1 Cause Multiple Morphological Abnormalities of the Sperm Flagella.
Martinez G et al.·Int J Mol Sci
2023
Novel mutations in FSIP2 cause male infertility through multiple morphological abnormalities of the sperm flagella.
Hussain M et al.·Asian J Androl
2026Case report
Bioinformatics analysis revealed hub genes and pathways involved in sorafenib resistance in hepatocellular carcinoma.
Liu J et al.·Math Biosci Eng
2019
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 6 full-text resultsSearch PubTator3 ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

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