TCF15

transcription factor 15, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 20:604256-610309

Links

ENSG00000125878 ∙ NCBI:6939 ∙ OMIM:601010 ∙ HGNC:11627 ∙ Uniprot:Q12870 ∙ 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 TCF15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCF15 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			14	3		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	3	0

Variants in TCF15

This is a list of pathogenic ClinVar variants found in the TCF15 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-604625-C-A		not specified	Uncertain significance (Apr 23, 2024)
20-604655-C-T		not specified	Uncertain significance (Feb 05, 2024)
20-609715-C-T		not specified	Uncertain significance (Jul 12, 2023)
20-609775-C-G		not specified	Likely benign (Apr 07, 2023)
20-609793-C-T		not specified	Likely benign (Apr 07, 2023)
20-609841-A-C		not specified	Likely benign (Apr 07, 2023)
20-609918-T-C		not specified	Uncertain significance (Dec 15, 2023)
20-610003-C-A		not specified	Uncertain significance (Sep 17, 2021)
20-610020-T-C		not specified	Uncertain significance (Nov 03, 2022)
20-610039-G-A		not specified	Uncertain significance (Dec 01, 2022)
20-610047-C-T		not specified	Uncertain significance (Dec 08, 2023)
20-610048-C-T		not specified	Uncertain significance (Jul 28, 2021)
20-610060-C-T		not specified	Uncertain significance (Apr 07, 2023)
20-610107-G-C		not specified	Uncertain significance (Oct 04, 2022)
20-610142-G-C		not specified	Uncertain significance (Aug 08, 2023)
20-610161-T-C		not specified	Uncertain significance (Nov 03, 2023)
20-610162-C-T		not specified	Uncertain significance (Nov 03, 2023)
20-610215-G-C		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCF15	protein_coding	protein_coding	ENST00000246080	2	6602

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.520	0.421	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	38	63.3	0.600	0.00000344	1158
Missense in Polyphen		10	27.248	0.367		473
Synonymous	0.672	23	27.5	0.837	0.00000136	434
Loss of Function	1.35	0	2.12	0.00	9.09e-8	42

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: May function as an early transcriptional regulator, involved in the patterning of the mesoderm and in lineage determination of cell types derived from the mesoderm.

Recessive Scores

• pRec: 0.159

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.490
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcf15
• Phenotype: craniofacial phenotype; muscle phenotype; growth/size/body region 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); 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); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype

Gene ontology

• Biological process: somitogenesis;respiratory system process;regulation of transcription by RNA polymerase II;mesoderm development;post-anal tail morphogenesis;eating behavior;ear development;skin development;establishment of epithelial cell apical/basal polarity;positive regulation of transcription by RNA polymerase II;paraxial mesoderm development;muscle organ morphogenesis;skeletal system morphogenesis;neuromuscular process controlling posture;mesenchymal to epithelial transition;regulation of extracellular matrix organization
• Cellular component: RNA polymerase II transcription factor complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein dimerization activity