IFT22

intraflagellar transport 22, the group of RAB like GTPases|IFT-B1 complex

Basic information

Region (hg38): 7:101310913-101321823

Previous symbols: [ "RABL5" ]

Links

ENSG00000128581 ∙ NCBI:64792 ∙ ∙ HGNC:21895 ∙ Uniprot:Q9H7X7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IFT22 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFT22 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in IFT22

This is a list of pathogenic ClinVar variants found in the IFT22 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-101315187-T-C		not specified	Uncertain significance (Apr 27, 2022)
7-101315219-C-T		not specified	Uncertain significance (May 27, 2022)
7-101316351-C-T		not specified	Likely benign (Mar 28, 2024)
7-101316357-T-C		not specified	Uncertain significance (Oct 26, 2021)
7-101316420-G-A		not specified	Uncertain significance (Aug 10, 2021)
7-101316462-C-T		not specified	Uncertain significance (May 17, 2023)
7-101316463-G-A		not specified	Uncertain significance (Jul 09, 2021)
7-101316466-G-C		not specified	Uncertain significance (Mar 31, 2022)
7-101316483-T-A		not specified	Uncertain significance (Sep 14, 2022)
7-101316507-G-A		not specified	Uncertain significance (Oct 02, 2023)
7-101316522-G-A		not specified	Uncertain significance (Oct 20, 2023)
7-101316531-C-T		not specified	Uncertain significance (Sep 28, 2022)
7-101318133-C-G		not specified	Uncertain significance (Jan 18, 2023)
7-101318204-T-G		not specified	Uncertain significance (Apr 12, 2022)
7-101318986-A-G		not specified	Uncertain significance (Jun 07, 2023)
7-101319029-C-T		not specified	Uncertain significance (May 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFT22	protein_coding	protein_coding	ENST00000315322	5	8130

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.336	0.651	125740	0	7	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.745	82	103	0.794	0.00000546	1236
Missense in Polyphen		24	31.762	0.75563		394
Synonymous	-0.402	43	39.8	1.08	0.00000230	327
Loss of Function	2.09	2	8.60	0.232	3.65e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Small GTPase-like component of the intraflagellar transport (IFT) complex B. {ECO:0000250}.
• Pathway: Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.324
• ghis: 0.614

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Ift22

Gene ontology

• Biological process: intracellular protein transport;Rab protein signal transduction;intraciliary transport involved in cilium assembly
• Cellular component: centrosome;cilium;intraciliary transport particle B;ciliary tip
• Molecular function: GTPase activity;GTP binding