TCF21

transcription factor 21, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 6:133889112-133895553

Links

ENSG00000118526 ∙ NCBI:6943 ∙ OMIM:603306 ∙ HGNC:11632 ∙ Uniprot:O43680 ∙ 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 TCF21 gene.

• Inborn genetic diseases (7 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCF21 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					2	2
missense			7			7
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	7	0	3

Variants in TCF21

This is a list of pathogenic ClinVar variants found in the TCF21 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-133889429-A-G		not specified	Uncertain significance (Mar 02, 2023)
6-133889439-G-T		not specified	Uncertain significance (May 16, 2022)
6-133889455-T-A		not specified	Uncertain significance (Jun 16, 2023)
6-133889460-C-G			Uncertain significance (Dec 01, 2014)
6-133889491-G-C		TCF21-related disorder	Likely benign (Sep 17, 2019)
6-133889667-C-T			Benign (Jul 12, 2018)
6-133889782-G-T		not specified	Uncertain significance (Aug 16, 2022)
6-133889809-G-A		not specified	Uncertain significance (Oct 26, 2022)
6-133889815-T-C		not specified	Uncertain significance (Sep 28, 2022)
6-133889838-G-T			Benign (Jul 07, 2018)
6-133889857-C-T		TCF21-related disorder	Likely benign (Oct 19, 2020)
6-133891457-A-G			Benign (Jun 19, 2021)
6-133891777-G-A		not specified	Uncertain significance (Dec 20, 2021)
6-133891783-G-A		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCF21	protein_coding	protein_coding	ENST00000367882	2	6416

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.826	0.171	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.780	79	101	0.782	0.00000466	1165
Missense in Polyphen		16	37.274	0.42926		400
Synonymous	0.165	43	44.4	0.968	0.00000221	360
Loss of Function	2.22	0	5.76	0.00	2.49e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in epithelial-mesenchymal interactions in kidney and lung morphogenesis that include epithelial differentiation and branching morphogenesis. May play a role in the specification or differentiation of one or more subsets of epicardial cell types.

Recessive Scores

• pRec: 0.247

Intolerance Scores

• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• pHI: 0.500
• hipred: Y
• hipred_score: 0.755
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcf21
• Phenotype: renal/urinary system phenotype; immune system phenotype; digestive/alimentary phenotype; neoplasm; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; respiratory system phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: tcf21
• Affected structure: interhyoideus
• Phenotype tag: abnormal
• Phenotype quality: hypoplastic

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;ureteric bud development;branching involved in ureteric bud morphogenesis;morphogenesis of a branching structure;kidney development;vasculature development;sex determination;branchiomeric skeletal muscle development;epithelial cell differentiation;glomerulus development;positive regulation of transcription by RNA polymerase II;lung alveolus development;spleen development;embryonic digestive tract morphogenesis;reproductive structure development;gland development;Sertoli cell differentiation;roof of mouth development;lung morphogenesis;lung vasculature development;bronchiole development;diaphragm development;respiratory system development;negative regulation of androgen receptor signaling pathway;metanephric mesenchymal cell differentiation;metanephric glomerular capillary formation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;histone deacetylase binding;bHLH transcription factor binding;protein dimerization activity;androgen receptor binding;E-box binding