TCF25

transcription factor 25

Basic information

Region (hg38): 16:89873569-89913627

Links

ENSG00000141002 ∙ NCBI:22980 ∙ OMIM:612326 ∙ HGNC:29181 ∙ Uniprot:Q9BQ70 ∙ 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 TCF25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCF25 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			50	8		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	50	9	1

Variants in TCF25

This is a list of pathogenic ClinVar variants found in the TCF25 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-89873697-G-C		not specified	Uncertain significance (Feb 14, 2023)
16-89873701-G-A		not specified	Uncertain significance (Jan 10, 2022)
16-89873708-G-A		not specified	Uncertain significance (Dec 15, 2023)
16-89873789-G-A		not specified	Uncertain significance (Dec 28, 2022)
16-89873812-G-A		not specified	Likely benign (Mar 05, 2024)
16-89873834-T-G		not specified	Uncertain significance (Jan 23, 2023)
16-89873853-C-G		not specified	Uncertain significance (Jan 17, 2023)
16-89883390-G-A		not specified	Uncertain significance (Feb 15, 2023)
16-89883406-G-C		not specified	Uncertain significance (Jun 10, 2022)
16-89883463-C-G		not specified	Uncertain significance (Dec 02, 2022)
16-89884588-G-T		not specified	Uncertain significance (Mar 13, 2023)
16-89884652-C-T		not specified	Uncertain significance (May 29, 2024)
16-89884654-T-C		not specified	Uncertain significance (Oct 05, 2022)
16-89884655-C-T		not specified	Uncertain significance (Dec 21, 2023)
16-89885854-G-A		not specified	Uncertain significance (Nov 27, 2023)
16-89885886-G-T		not specified	Uncertain significance (Jun 11, 2021)
16-89885891-A-G		not specified	Uncertain significance (Jul 12, 2023)
16-89885896-A-G		not specified	Uncertain significance (Nov 10, 2022)
16-89885912-G-A		not specified	Likely benign (Dec 02, 2021)
16-89885947-G-C		not specified	Uncertain significance (Jun 30, 2022)
16-89892218-C-G		not specified	Uncertain significance (Aug 17, 2022)
16-89892249-G-A		not specified	Uncertain significance (Aug 19, 2021)
16-89892272-C-T		not specified	Uncertain significance (Jul 09, 2021)
16-89895129-A-C		not specified	Uncertain significance (Apr 20, 2024)
16-89895996-C-T		not specified	Uncertain significance (Jan 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCF25	protein_coding	protein_coding	ENST00000263346	18	37793

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.416	0.584	125730	0	16	125746	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0382	424	422	1.01	0.0000267	4382
Missense in Polyphen		86	101.52	0.84715		1092
Synonymous	-2.16	216	179	1.21	0.0000124	1320
Loss of Function	4.32	8	35.9	0.223	0.00000168	409

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000890	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in cell death control. Acts as a transcriptional repressor. Has been shown to repress transcription of SRF in vitro and so may play a role in heart development. {ECO:0000269|PubMed:16574069}.

Intolerance Scores

• loftool: 0.150
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.2

Haploinsufficiency Scores

• pHI: 0.204
• hipred: N
• hipred_score: 0.492
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.760

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcf25

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;heart development
• Cellular component: nucleus
• Molecular function: DNA binding;DNA-binding transcription factor activity;protein binding