IFTAP

intraflagellar transport associated protein

Basic information

Region (hg38): 11:36594369-36675695

Previous symbols: [ "C11orf74" ]

Links

ENSG00000166352 ∙ NCBI:119710 ∙ OMIM:619270 ∙ HGNC:25142 ∙ Uniprot:Q86VG3 ∙ 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 IFTAP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFTAP 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1	3	6
Total	0	0	6	1	3

Variants in IFTAP

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

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

Position	Type	Phenotype	Significance	ClinVar
11-36594508-G-C			Benign (Nov 14, 2019)
11-36595228-C-T			Benign (Jun 23, 2018)
11-36598211-A-G		Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive • Histiocytic medullary reticulosis	Benign (Jul 11, 2018)
11-36598220-C-A		Histiocytic medullary reticulosis • Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive	Uncertain significance (Jan 13, 2018)
11-36598225-T-G		Histiocytic medullary reticulosis • Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive	Uncertain significance (Jan 13, 2018)
11-36598299-CT-C			Likely benign (Aug 12, 2018)
11-36633290-A-G		not specified	Uncertain significance (Aug 10, 2021)
11-36633308-T-G		not specified	Uncertain significance (Jul 06, 2021)
11-36633362-A-T		not specified	Uncertain significance (Aug 13, 2021)
11-36636083-C-A		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFTAP	protein_coding	protein_coding	ENST00000532470	5	78773

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000761	0.310	125725	0	17	125742	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.186	112	107	1.05	0.00000474	1485
Missense in Polyphen		29	24.602	1.1788		389
Synonymous	-0.0884	37	36.3	1.02	0.00000165	371
Loss of Function	0.142	8	8.45	0.947	3.55e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000102	0.000102
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000105
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0735

Intolerance Scores

• loftool: 0.391
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.82

Haploinsufficiency Scores

• pHI: 0.0596
• hipred: N
• hipred_score: 0.123
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B230118H07Rik

Gene ontology

• Cellular component: cilium