CTIF

cap binding complex dependent translation initiation factor, the group of MIF4G domain containing proteins|MicroRNA protein coding host genes

Basic information

Region (hg38): 18:48539030-48863217

Previous symbols: [ "KIAA0427" ]

Links

ENSG00000134030 ∙ NCBI:9811 ∙ OMIM:613178 ∙ HGNC:23925 ∙ Uniprot:O43310 ∙ 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 CTIF gene.

• Inborn genetic diseases (25 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTIF 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	2	3
missense			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	24	2	2

Variants in CTIF

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

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

Position	Type	Phenotype	Significance	ClinVar
18-48619609-G-A		not specified	Uncertain significance (Apr 22, 2022)
18-48619615-G-A		not specified	Uncertain significance (Jan 09, 2024)
18-48619650-G-A		not specified	Uncertain significance (May 27, 2022)
18-48619673-G-C		not specified	Uncertain significance (Feb 16, 2023)
18-48619680-G-A		not specified	Uncertain significance (Jul 14, 2021)
18-48619718-C-T			Likely benign (Mar 01, 2022)
18-48619734-C-T		not specified	Uncertain significance (Oct 20, 2023)
18-48636622-G-A			Benign (Aug 08, 2018)
18-48636636-C-T		not specified	Uncertain significance (Sep 22, 2023)
18-48663815-G-A		not specified	Uncertain significance (Jun 17, 2022)
18-48663829-A-G			Benign (Aug 08, 2018)
18-48664477-G-C		not specified	Uncertain significance (Feb 22, 2023)
18-48664499-C-A		not specified	Uncertain significance (Jun 21, 2023)
18-48664537-C-G		not specified	Uncertain significance (Nov 09, 2022)
18-48664545-G-A		not specified	Uncertain significance (Dec 12, 2023)
18-48670721-G-A		not specified	Uncertain significance (Jun 22, 2023)
18-48757936-C-T		not specified	Uncertain significance (Jul 27, 2021)
18-48757989-C-A		not specified	Uncertain significance (Jun 28, 2022)
18-48757996-G-A		not specified	Uncertain significance (Aug 28, 2023)
18-48758018-G-C		not specified	Uncertain significance (Apr 11, 2023)
18-48758076-C-T		not specified	Uncertain significance (Nov 17, 2023)
18-48758090-T-G		not specified	Uncertain significance (Feb 16, 2023)
18-48758095-A-C		not specified	Uncertain significance (Feb 16, 2023)
18-48758133-G-A		not specified	Likely benign (Nov 08, 2021)
18-48758146-C-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTIF	protein_coding	protein_coding	ENST00000382998	11	324172

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000618	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	297	379	0.784	0.0000247	3943
Missense in Polyphen		48	100.26	0.47878		1083
Synonymous	-0.789	171	158	1.08	0.0000108	1162
Loss of Function	4.86	0	27.5	0.00	0.00000137	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000920	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000194	0.000185
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically required for the pioneer round of mRNA translation mediated by the cap-binding complex (CBC), that takes place during or right after mRNA export via the nuclear pore complex (NPC). Acts via its interaction with the NCBP1/CBP80 component of the CBC complex and recruits the 40S small subunit of the ribosome via eIF3. In contrast, it is not involved in steady state translation, that takes place when the CBC complex is replaced by cytoplasmic cap-binding protein eIF4E. Also required for nonsense-mediated mRNA decay (NMD), the pioneer round of mRNA translation mediated by the cap-binding complex playing a central role in nonsense-mediated mRNA decay (NMD). {ECO:0000269|PubMed:19648179}.

Intolerance Scores

• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.83

Haploinsufficiency Scores

• pHI: 0.462
• hipred: Y
• hipred_score: 0.591
• ghis: 0.567

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: Ctif

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;regulation of translational initiation;positive regulation of translation
• Cellular component: cytosol;perinuclear region of cytoplasm
• Molecular function: RNA binding;protein binding;translation activator activity