TFPT

TCF3 fusion partner, the group of INO80 complex

Basic information

Region (hg38): 19:54107020-54115657

Links

ENSG00000105619 ∙ NCBI:29844 ∙ OMIM:609519 ∙ HGNC:13630 ∙ Uniprot:P0C1Z6 ∙ 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 TFPT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TFPT 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	2		3
Total	0	0	19	2	0

Variants in TFPT

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

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

Position	Type	Phenotype	Significance	ClinVar
19-54107096-T-C		not specified	Uncertain significance (Jun 30, 2022)
19-54107144-A-G		not specified	Uncertain significance (May 13, 2024)
19-54108069-C-T		not specified	Uncertain significance (Jan 26, 2023)
19-54108078-C-T		not specified	Uncertain significance (May 30, 2024)
19-54108087-C-T		not specified	Uncertain significance (Jul 25, 2023)
19-54108091-G-A		not specified	Uncertain significance (Dec 26, 2023)
19-54108093-C-A		not specified	Uncertain significance (Mar 19, 2024)
19-54108145-G-A		not specified	Uncertain significance (Sep 06, 2022)
19-54108229-C-T		not specified	Uncertain significance (Mar 15, 2024)
19-54108354-C-T		not specified	Uncertain significance (Dec 18, 2023)
19-54108355-G-A		not specified	Uncertain significance (Mar 23, 2022)
19-54108367-C-T		not specified	Uncertain significance (Nov 17, 2023)
19-54108382-C-G		not specified	Uncertain significance (Jan 26, 2023)
19-54108387-A-G		not specified	Uncertain significance (Dec 19, 2022)
19-54110058-C-G		not specified	Uncertain significance (Apr 22, 2022)
19-54110098-C-G		not specified	Uncertain significance (Mar 24, 2023)
19-54110114-T-A		not specified	Uncertain significance (Jul 19, 2022)
19-54114455-C-T		not specified	Uncertain significance (May 20, 2024)
19-54114474-C-A		not specified	Uncertain significance (Jan 17, 2023)
19-54114518-C-A		not specified	Uncertain significance (Mar 23, 2022)
19-54114533-T-G		not specified	Uncertain significance (Mar 19, 2024)
19-54114535-C-G		not specified	Uncertain significance (Jul 14, 2023)
19-54114579-A-T		not specified	Uncertain significance (Jun 04, 2024)
19-54114653-G-A		not specified	Uncertain significance (Mar 28, 2024)
19-54114699-T-C		not specified	Uncertain significance (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TFPT	protein_coding	protein_coding	ENST00000391759	6	8736

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000106	0.827	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.462	146	163	0.898	0.0000102	1582
Missense in Polyphen		25	33.126	0.75469		415
Synonymous	-0.521	72	66.6	1.08	0.00000374	555
Loss of Function	1.25	8	12.9	0.622	7.17e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000519	0.000510
Ashkenazi Jewish	0.00	0.00
East Asian	0.000226	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000641	0.0000527
Middle Eastern	0.000226	0.000217
South Asian	0.000134	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Appears to promote apoptosis in a p53/TP53-independent manner.
• Disease: DISEASE: Note=A chromosomal aberration involving TFPT is a cause of pre-B-cell acute lymphoblastic leukemia (B-ALL). Inversion inv(19)(p13;q13) with TCF3. {ECO:0000269|PubMed:10086727}.
• Pathway: DNA Repair;Post-translational protein modification;Metabolism of proteins;UCH proteinases;Deubiquitination;DNA Damage Recognition in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Nucleotide Excision Repair (Consensus)

Recessive Scores

• pRec: 0.271

Intolerance Scores

• loftool: 0.306
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.174
• hipred: N
• hipred_score: 0.297
• ghis: 0.528

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tfpt

Gene ontology

• Biological process: DNA repair;DNA recombination;apoptotic process;protein deubiquitination;apoptotic signaling pathway
• Cellular component: nucleus;nucleoplasm;cytoplasm;Ino80 complex;nuclear membrane
• Molecular function: DNA binding;protein binding