IFT88

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

Basic information

Region (hg38): 13:20567137-20691444

Previous symbols: [ "TTC10" ]

Links

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

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.

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.

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			2	56	6	64
missense			200	8	10	218
nonsense			2			2
start loss			2			2
frameshift			7			7
inframe indel			1			1
splice donor/acceptor (+/-2bp)			3			3
splice region			7	15	3	25
non coding			5	70	14	89
Total	0	0	222	134	30

Variants in IFT88

This is a list of pathogenic ClinVar variants found in the IFT88 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-20567683-A-G			Benign (Jun 14, 2021)
13-20567977-A-G			Uncertain significance (Feb 09, 2022)
13-20567992-A-G			Uncertain significance (Dec 18, 2023)
13-20567995-A-G			Uncertain significance (Dec 26, 2022)
13-20568002-C-T			Likely benign (Jan 20, 2024)
13-20568007-G-A			Likely benign (Dec 17, 2023)
13-20568013-T-TA			Benign (Jun 09, 2023)
13-20574368-A-G			Uncertain significance (Aug 07, 2022)
13-20574369-G-A			Uncertain significance (Jun 01, 2022)
13-20574386-A-G			Uncertain significance (Nov 11, 2022)
13-20574403-C-G			Uncertain significance (Sep 10, 2022)
13-20574410-C-T		not specified	Uncertain significance (May 04, 2023)
13-20574439-C-T			Likely benign (Feb 18, 2022)
13-20574451-C-T			Likely benign (Mar 26, 2022)
13-20574453-A-G			Uncertain significance (Sep 27, 2022)
13-20574456-A-G		not specified	Uncertain significance (Sep 20, 2023)
13-20574459-C-T		not specified	Uncertain significance (May 05, 2023)
13-20574464-T-G			Uncertain significance (Feb 17, 2022)
13-20574465-A-C			Uncertain significance (Oct 13, 2022)
13-20574471-T-C		IFT88-related disorder	Likely benign (Oct 18, 2023)
13-20574472-C-T			Likely benign (Nov 01, 2022)
13-20574473-G-A			Uncertain significance (Sep 10, 2022)
13-20582943-C-T			Likely benign (Oct 15, 2023)
13-20582944-G-A			Likely benign (Mar 21, 2023)
13-20582957-G-A			Uncertain significance (Jan 02, 2022)

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
7.12e-11	1.00	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

Haploinsufficiency Scores

• pHI: 0.396
• hipred: N
• hipred_score: 0.414
• ghis: 0.532

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

Mouse Genome Informatics

• Gene name: Ift88
• Phenotype: respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; renal/urinary system phenotype; skeleton phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); craniofacial phenotype

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