IFT70A

intraflagellar transport 70A, the group of IFT-B1 complex|Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 2:177612999-177618742

Previous symbols: [ "TTC30A" ]

Links

ENSG00000197557 ∙ NCBI:92104 ∙ ∙ HGNC:25853 ∙ Uniprot:Q86WT1 ∙ 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 IFT70A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFT70A 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			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	0	0

Variants in IFT70A

This is a list of pathogenic ClinVar variants found in the IFT70A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-177616712-T-G		not specified	Uncertain significance (Oct 26, 2022)
2-177616777-C-T		not specified	Uncertain significance (May 17, 2023)
2-177616859-A-G		not specified	Uncertain significance (Feb 27, 2023)
2-177616907-T-G		not specified	Uncertain significance (May 02, 2024)
2-177616919-C-T		not specified	Uncertain significance (Dec 16, 2022)
2-177617036-C-T		not specified	Uncertain significance (Feb 13, 2023)
2-177617100-A-T		not specified	Uncertain significance (Dec 06, 2023)
2-177617230-T-C		not specified	Uncertain significance (Oct 03, 2022)
2-177617267-T-C		not specified	Uncertain significance (Oct 06, 2021)
2-177617351-C-G		not specified	Uncertain significance (Nov 02, 2023)
2-177617380-G-A		not specified	Uncertain significance (Aug 08, 2023)
2-177617432-T-C		not specified	Uncertain significance (May 07, 2024)
2-177617480-C-G		not specified	Uncertain significance (Aug 13, 2021)
2-177617497-T-C		not specified	Uncertain significance (Jan 03, 2024)
2-177617509-T-C		not specified	Uncertain significance (Apr 25, 2023)
2-177617513-C-T		not specified	Uncertain significance (Jul 12, 2023)
2-177617528-T-C		not specified	Uncertain significance (Apr 18, 2024)
2-177617542-G-C		not specified	Uncertain significance (Dec 18, 2023)
2-177617732-C-T		not specified	Uncertain significance (Jan 02, 2024)
2-177617814-C-G		not specified	Uncertain significance (Mar 01, 2024)
2-177617840-C-G		not specified	Uncertain significance (Feb 03, 2022)
2-177617867-G-A		not specified	Uncertain significance (Apr 28, 2023)
2-177617890-T-C		not specified	Uncertain significance (Feb 14, 2023)
2-177617975-A-C		not specified	Uncertain significance (Oct 27, 2023)
2-177618093-C-A		not specified	Likely benign (Apr 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFT70A	protein_coding	protein_coding	ENST00000355689	1	5975

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.46e-7	0.872	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.613	375	343	1.09	0.0000167	4328
Missense in Polyphen		72	91.794	0.78437		1212
Synonymous	-1.32	162	142	1.14	0.00000707	1297
Loss of Function	1.56	13	20.7	0.629	0.00000104	279

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for polyglutamylation of axonemal tubulin. Plays a role in anterograde intraflagellar transport (IFT), the process by which cilia precursors are transported from the base of the cilium to the site of their incorporation at the tip. {ECO:0000250}.
• Pathway: Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Intolerance Scores

• loftool: 0.683
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.71

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.438

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc30a2

Gene ontology

• Biological process: intraciliary transport
• Cellular component: cilium;intraciliary transport particle B