IFT88

intraflagellar transport 88, the group of IFT-B1 complex|Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 13:20567138-20691444

Previous symbols: [ "TTC10" ]

Links

ENSG00000032742 ∙ NCBI:8100 ∙ OMIM:600595 ∙ HGNC:20606 ∙ Uniprot:Q13099 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 101.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
ENST00000319980.10	ENSP00000323580.6	26	-	-
ENST00000351808.10	ENSP00000261632.5	25	yes	-
ENST00000389373.3	ENSP00000374024.3	2	-	-
ENST00000537103.2	ENSP00000437719.2	11	-	-

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliopathy, IFT88-related	AR	General	Individuals may have renal and hepatic manifestations in this reported lethal disorder; Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Gastrointestinal; Neurologic; Renal	22941275

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IFT88 gene.

• not_provided (506 variants)
• not_specified (94 variants)
• IFT88-related_disorder (20 variants)
• Rod-cone_dystrophy (2 variants)
• Jeune_thoracic_dystrophy (1 variants)
• See_cases (1 variants)
• Retinitis_pigmentosa (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFT88 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006531.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	76	7	86
missense		1	292	11	8	312
nonsense			6			6
start loss			1			1
frameshift		1	14			15
splice donor/acceptor (+/-2bp)			20			20
Total	0	2	336	87	15

Highest pathogenic variant AF is 0.0000021988137

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFT88	protein_coding	protein_coding	ENST00000319980	26	124919

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125668	0	80	125748	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.335	394	413	0.954	0.0000201	5478
Missense in Polyphen		65	83.894	0.77479		1115
Synonymous	0.982	122	137	0.893	0.00000673	1456
Loss of Function	3.21	25	49.3	0.507	0.00000245	683

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000829	0.000784
Ashkenazi Jewish	0.000202	0.000198
East Asian	0.000275	0.000272
Finnish	0.0000940	0.0000924
European (Non-Finnish)	0.000426	0.000404
Middle Eastern	0.000275	0.000272
South Asian	0.000321	0.000294
Other	0.000197	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in primary cilium biogenesis. Also involved in autophagy since it is required for trafficking of ATG16L and the expansion of the autophagic compartment. {ECO:0000250|UniProtKB:Q61371}.
• Pathway: Endochondral Ossification;Hedgehog signaling events mediated by Gli proteins;Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.635
• rvis_EVS: -0.26
• rvis_percentile_EVS: 34.93

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.817

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Zebrafish Information Network

• Gene name: ift88
• Affected structure: neuromast hair cell
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: kidney development;intraciliary transport involved in cilium assembly;inner ear receptor cell stereocilium organization;cilium assembly;regulation of cilium assembly;non-motile cilium assembly;regulation of autophagosome assembly
• Cellular component: centrosome;centriole;cilium;intraciliary transport particle B;motile cilium;ciliary basal body;sperm flagellum;ciliary tip;ciliary base;non-motile cilium
• Molecular function: protein binding;kinesin binding