TFEC

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

Basic information

Region (hg38): 7:115935147-116159896

Links

ENSG00000105967 ∙ NCBI:22797 ∙ OMIM:604732 ∙ HGNC:11754 ∙ Uniprot:O14948 ∙ 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 TFEC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TFEC 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			15	1	1	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	15	1	3

Variants in TFEC

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

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

Position	Type	Phenotype	Significance	ClinVar
7-115940676-T-C		not specified	Uncertain significance (Aug 17, 2022)
7-115940732-T-C		not specified	Uncertain significance (May 29, 2024)
7-115940745-C-T		not specified	Uncertain significance (Apr 09, 2024)
7-115940756-A-C		not specified	Uncertain significance (Feb 28, 2024)
7-115940760-C-G		not specified	Uncertain significance (Sep 20, 2023)
7-115940829-G-T		not specified	Uncertain significance (Nov 09, 2021)
7-115940912-C-T		not specified	Uncertain significance (Jan 19, 2024)
7-115941904-G-A		not specified	Uncertain significance (Apr 04, 2024)
7-115941935-C-A		not specified	Uncertain significance (Mar 31, 2022)
7-115941983-C-A		not specified	Uncertain significance (Sep 22, 2022)
7-115942033-G-A		not specified	Uncertain significance (Dec 07, 2021)
7-115942035-A-G		not specified	Uncertain significance (Sep 13, 2023)
7-115954618-T-C		not specified	Uncertain significance (Sep 25, 2023)
7-115954621-G-C		not specified	Uncertain significance (Nov 09, 2023)
7-115954636-T-A		not specified	Uncertain significance (Jun 29, 2023)
7-115956742-T-C		not specified	Likely benign (Dec 03, 2021)
7-115956746-T-G			Benign (Jan 08, 2018)
7-115956763-C-T			Benign (Dec 28, 2017)
7-115956792-A-G		not specified	Uncertain significance (Jun 13, 2024)
7-115974225-A-G		not specified	Uncertain significance (May 29, 2024)
7-115974247-C-T		not specified	Uncertain significance (Jan 23, 2024)
7-115984315-G-A		not specified	Uncertain significance (Jan 20, 2023)
7-115984385-C-T			Benign (Jan 08, 2018)
7-115984416-T-C		not specified	Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TFEC	protein_coding	protein_coding	ENST00000265440	7	224749

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.28e-8	0.599	125675	1	65	125741	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0922	182	179	1.02	0.00000861	2263
Missense in Polyphen		48	54.799	0.87593		739
Synonymous	-0.979	73	63.1	1.16	0.00000306	659
Loss of Function	1.12	14	19.3	0.726	0.00000112	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00225	0.00219
Ashkenazi Jewish	0.00	0.00
East Asian	0.000388	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.0000622	0.0000615
Middle Eastern	0.000388	0.000381
South Asian	0.0000663	0.0000653
Other	0.000849	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator that acts as a repressor or an activator. Acts as a transcriptional repressor on minimal promoter containing element F (that includes an E-box sequence). Binds to element F in an E-box sequence-specific manner. Acts as a transcriptional transactivator on the proximal promoter region of the tartrate-resistant acid phosphatase (TRAP) E-box containing promoter (By similarity). Collaborates with MITF in target gene activation (By similarity). Acts as a transcriptional repressor on minimal promoter containing mu E3 enhancer sequence (By similarity). Binds to mu E3 DNA sequence of the immunoglobulin heavy-chain gene enhancer (By similarity). Binds DNA in a homo- or heterodimeric form. {ECO:0000250, ECO:0000269|PubMed:11467950, ECO:0000269|PubMed:9256061}.
• Pathway: C-MYB transcription factor network (Consensus)

Recessive Scores

• pRec: 0.183

Intolerance Scores

• loftool: 0.410
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.288
• hipred: N
• hipred_score: 0.304
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.657

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tfec
• Phenotype: homeostasis/metabolism 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); skeleton phenotype; vision/eye phenotype; normal phenotype; pigmentation phenotype

Zebrafish Information Network

• Gene name: tfec
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: cellular response to heat;positive regulation of transcription by RNA polymerase II;negative regulation of nucleic acid-templated transcription
• Cellular component: nucleoplasm
• 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;transcription coactivator activity;transcription corepressor activity;protein binding;protein dimerization activity