TCF23

transcription factor 23, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 2:27149003-27156974

Links

ENSG00000163792 ∙ NCBI:150921 ∙ OMIM:609635 ∙ HGNC:18602 ∙ Uniprot:Q7RTU1 ∙ 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 TCF23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCF23 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in TCF23

This is a list of pathogenic ClinVar variants found in the TCF23 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27149153-G-A		not specified	Uncertain significance (Mar 17, 2023)
2-27149218-G-A		not specified	Uncertain significance (Dec 20, 2023)
2-27149221-G-A		not specified	Likely benign (Jun 17, 2024)
2-27149354-G-C		not specified	Uncertain significance (Mar 29, 2022)
2-27150147-G-A		not specified	Uncertain significance (Feb 05, 2024)
2-27150148-C-T		not specified	Uncertain significance (Aug 30, 2022)
2-27150151-G-A		not specified	Uncertain significance (Dec 20, 2023)
2-27150172-C-T		not specified	Uncertain significance (Aug 10, 2021)
2-27150178-G-A		not specified	Uncertain significance (Dec 15, 2023)
2-27150213-G-C		not specified	Uncertain significance (May 18, 2022)
2-27150234-C-T		not specified	Uncertain significance (Jun 21, 2022)
2-27150288-C-T		not specified	Uncertain significance (Nov 19, 2022)
2-27150298-G-A		not specified	Uncertain significance (Aug 16, 2021)
2-27150303-G-A		not specified	Uncertain significance (Jul 14, 2021)
2-27150346-G-A		not specified	Uncertain significance (Nov 12, 2021)
2-27150353-G-T		not specified	Uncertain significance (Dec 27, 2023)
2-27152695-C-T		not specified	Uncertain significance (Jun 21, 2021)
2-27152701-G-A		not specified	Uncertain significance (Sep 14, 2022)
2-27152746-C-T		not specified	Uncertain significance (Dec 01, 2022)
2-27152761-C-A		not specified	Uncertain significance (Nov 06, 2023)
2-27152788-A-G		not specified	Uncertain significance (Dec 07, 2023)
2-27152821-C-T		not specified	Uncertain significance (Mar 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCF23	protein_coding	protein_coding	ENST00000296096	3	4507

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000442	0.422	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.761	115	140	0.819	0.00000936	1337
Missense in Polyphen		40	45.508	0.87897		425
Synonymous	0.0475	58	58.5	0.992	0.00000392	482
Loss of Function	0.302	7	7.92	0.884	4.87e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000430	0.000371
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000448	0.0000439
Middle Eastern	0.000218	0.000217
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits E-box-mediated binding and transactivation of bHLH factors. Inhibitory effect is similar to that of ID proteins. Inhibits the formation of TCF3 and MYOD1 homodimers and heterodimers. Lacks DNA binding activity. Seems to play a role in the inhibition of myogenesis (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.330
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.582
• hipred: N
• hipred_score: 0.220

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcf23

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;muscle organ development;positive regulation of gene expression;cell differentiation;decidualization
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein dimerization activity