IFT43

intraflagellar transport 43, the group of IFT-A complex

Basic information

Region (hg38): 14:75902136-76084585

Previous symbols: [ "C14orf179" ]

Links

ENSG00000119650 ∙ NCBI:112752 ∙ OMIM:614068 ∙ HGNC:29669 ∙ Uniprot:Q96FT9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cranioectodermal dysplasia 3 (Definitive), mode of inheritance: AR
• cranioectodermal dysplasia (Supportive), mode of inheritance: AR
• short-rib thoracic dysplasia 18 with polydactyly (Strong), mode of inheritance: AR
• retinitis pigmentosa 81 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cranioectodermal dysplasia 3; Retinitis pigmentosa 81; Short-rib thoracic dysplasia 18 with polydactyly	AR	General	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	Craniofacial; Dental; Dermatologic; Musculoskeletal; Neurologic; Ophthalmologic; Renal	21378380; 28400947; 28973684

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IFT43 gene.

• not provided (12 variants)
• Short-rib thoracic dysplasia 18 with polydactyly (1 variants)
• Cranioectodermal dysplasia 3 (1 variants)
• Short rib-polydactyly syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFT43 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			1	47	1	49
missense		1	72	5	4	82
nonsense	3		1			4
start loss	3					3
frameshift	6		1			7
inframe indel			2			2
splice donor/acceptor (+/-2bp)		5	1			6
splice region		1	7	8	1	17
non coding		1	2	60	16	79
Total	12	7	80	112	21

Highest pathogenic variant AF is 0.0000657

Variants in IFT43

This is a list of pathogenic ClinVar variants found in the IFT43 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-75902142-A-AG			Uncertain significance (Sep 13, 2022)
14-75902148-C-T			Likely benign (Mar 19, 2022)
14-75902151-C-T			Likely benign (Nov 08, 2022)
14-75902152-G-A			Uncertain significance (Sep 01, 2021)
14-75902153-C-T		Inborn genetic diseases	Uncertain significance (Jan 19, 2024)
14-75902154-G-A			Uncertain significance (Jan 27, 2021)
14-75902157-A-G			Likely benign (Jul 16, 2023)
14-75902159-G-C		Inborn genetic diseases	Conflicting classifications of pathogenicity (Sep 28, 2022)
14-75902161-C-T			Pathogenic (May 16, 2022)
14-75902173-C-T		Inborn genetic diseases	Uncertain significance (Nov 13, 2023)
14-75902174-T-C			Uncertain significance (Mar 26, 2020)
14-75902178-G-A		TTLL5-related disorder	Benign (Jan 23, 2024)
14-75902179-A-G			Uncertain significance (Apr 16, 2021)
14-75902180-G-A			Uncertain significance (Apr 24, 2022)
14-75902181-C-A		Inborn genetic diseases	Uncertain significance (Jan 16, 2024)
14-75902186-T-C		Inborn genetic diseases	Uncertain significance (Oct 01, 2022)
14-75902195-C-T			Uncertain significance (May 16, 2022)
14-75902201-T-C			Benign (Jan 31, 2024)
14-75902204-T-C			Uncertain significance (Aug 10, 2023)
14-75902205-G-A			Likely benign (Aug 19, 2022)
14-75902206-C-T			Uncertain significance (Aug 22, 2022)
14-75902207-C-T			Uncertain significance (Mar 09, 2022)
14-75902208-C-T			Likely benign (Dec 14, 2022)
14-75902213-C-A			Uncertain significance (May 17, 2021)
14-75902213-C-G			Uncertain significance (Dec 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFT43	protein_coding	protein_coding	ENST00000238628	8	182450

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.82e-11	0.0328	125586	0	162	125748	0.000644

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.296	132	123	1.08	0.00000792	1383
Missense in Polyphen		39	39.604	0.98476		451
Synonymous	-0.992	58	49.1	1.18	0.00000337	406
Loss of Function	-0.213	16	15.1	1.06	8.43e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000886	0.000886
Ashkenazi Jewish	0.000992	0.000993
East Asian	0.000326	0.000326
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000669	0.000668
Middle Eastern	0.000326	0.000326
South Asian	0.00111	0.00111
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As a component of IFT complex A (IFT-A), it is involved in ciliogenesis (PubMed:28400947, PubMed:28973684). Involved in retrograde ciliary transport along microtubules from the ciliary tip to the base (PubMed:21378380). {ECO:0000269|PubMed:21378380, ECO:0000269|PubMed:28400947, ECO:0000269|PubMed:28973684}.
• Disease: DISEASE: Retinitis pigmentosa 81 (RP81) [MIM:617871]: A form of retinitis pigmentosa, a retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. RP81 inheritance is autosomal recessive. {ECO:0000269|PubMed:28973684}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Short-rib thoracic dysplasia 18 with polydactyly (SRTD18) [MIM:617866]: A form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a 'trident' appearance of the acetabular roof. Polydactyly is variably present. Non-skeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of the disease are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life. Disease spectrum encompasses Ellis-van Creveld syndrome, asphyxiating thoracic dystrophy (Jeune syndrome), Mainzer-Saldino syndrome, and short rib-polydactyly syndrome. {ECO:0000269|PubMed:28400947}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.248
• hipred: N
• hipred_score: 0.170
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ift43

Gene ontology

• Biological process: intraciliary retrograde transport;intraciliary transport involved in cilium assembly;cilium assembly
• Cellular component: cytoplasm;microtubule organizing center;cilium;microtubule cytoskeleton;intraciliary transport particle A;ciliary tip
• Molecular function: protein binding