TFIP11

tuftelin interacting protein 11, the group of G-patch domain containing|Spliceosomal B complex

Basic information

Region (hg38): 22:26491224-26512505

Links

ENSG00000100109 ∙ NCBI:24144 ∙ OMIM:612747 ∙ HGNC:17165 ∙ Uniprot:Q9UBB9 ∙ 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 TFIP11 gene.

• Inborn genetic diseases (27 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TFIP11 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		1
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	27	2	0

Variants in TFIP11

This is a list of pathogenic ClinVar variants found in the TFIP11 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-26491530-C-T		not specified	Uncertain significance (Feb 21, 2024)
22-26492178-C-A		not specified	Uncertain significance (Sep 06, 2022)
22-26492236-A-G		not specified	Uncertain significance (Jun 16, 2022)
22-26492239-C-G		not specified	Uncertain significance (Feb 07, 2023)
22-26492279-C-T		not specified	Uncertain significance (Jul 26, 2022)
22-26492344-C-T		not specified	Uncertain significance (Aug 19, 2023)
22-26494819-T-A		not specified	Uncertain significance (Jun 22, 2023)
22-26494823-T-C		not specified	Uncertain significance (Jan 24, 2024)
22-26494856-T-C		not specified	Uncertain significance (Oct 26, 2022)
22-26494895-T-C		not specified	Uncertain significance (Aug 02, 2021)
22-26494939-C-T		not specified	Uncertain significance (Mar 07, 2023)
22-26496156-T-C		not specified	Uncertain significance (Jan 22, 2024)
22-26496211-G-A		not specified	Uncertain significance (May 31, 2023)
22-26496818-G-A		not specified	Uncertain significance (May 24, 2023)
22-26496857-C-T		not specified	Uncertain significance (Dec 01, 2022)
22-26498900-C-G		not specified	Uncertain significance (Dec 22, 2023)
22-26498958-G-A			Likely benign (Mar 01, 2023)
22-26498959-G-A		not specified	Uncertain significance (Jun 12, 2023)
22-26498975-C-T		not specified	Uncertain significance (Sep 13, 2023)
22-26499121-C-T		not specified	Uncertain significance (Aug 12, 2022)
22-26499228-C-T		not specified	Uncertain significance (Sep 27, 2022)
22-26499229-G-A		not specified	Uncertain significance (Sep 22, 2021)
22-26499280-G-A		not specified	Uncertain significance (Jun 27, 2022)
22-26499291-T-C		not specified	Uncertain significance (Apr 18, 2023)
22-26499478-C-T		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TFIP11	protein_coding	protein_coding	ENST00000407690	12	21281

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.66e-12	0.986	125625	0	123	125748	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.35	415	500	0.830	0.0000302	5590
Missense in Polyphen		84	127.24	0.66017		1484
Synonymous	-0.764	206	193	1.07	0.0000122	1516
Loss of Function	2.48	26	43.7	0.595	0.00000221	465

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00123	0.00123
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000272	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000493	0.000484
Middle Eastern	0.000272	0.000272
South Asian	0.000490	0.000490
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing, specifically in spliceosome disassembly during late-stage splicing events. Intron turnover seems to proceed through reactions in two lariat-intron associated complexes termed Intron Large (IL) and Intron Small (IS). In cooperation with DHX15 seems to mediate the transition of the U2, U5 and U6 snRNP-containing IL complex to the snRNP-free IS complex leading to efficient debranching and turnover of excised introns. May play a role in the differentiation of ameloblasts and odontoblasts or in the forming of the enamel extracellular matrix. {ECO:0000269|PubMed:19103666}.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.875
• rvis_EVS: -1.52
• rvis_percentile_EVS: 3.42

Haploinsufficiency Scores

• pHI: 0.175
• hipred: Y
• hipred_score: 0.575
• ghis: 0.546

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.922

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tfip11

Gene ontology

• Biological process: spliceosomal complex disassembly;mRNA splicing, via spliceosome;RNA processing;biomineral tissue development;negative regulation of protein complex assembly;protection from non-homologous end joining at telomere;negative regulation of protein binding;negative regulation of DNA ligase activity;negative regulation of double-strand break repair via nonhomologous end joining
• Cellular component: nuclear chromosome, telomeric region;nucleoplasm;spliceosomal complex;nucleolus;cytoplasm;nuclear speck;extracellular matrix;U2-type post-mRNA release spliceosomal complex;catalytic step 2 spliceosome
• Molecular function: nucleic acid binding;protein binding