TCFL5

transcription factor like 5, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 20:62841005-62861822

Links

ENSG00000101190 ∙ NCBI:10732 ∙ OMIM:604745 ∙ HGNC:11646 ∙ Uniprot:Q9UL49 ∙ 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 TCFL5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCFL5 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			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	33	2	0

Variants in TCFL5

This is a list of pathogenic ClinVar variants found in the TCFL5 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-62841051-A-C		Multiple Epiphyseal Dysplasia, Dominant	Uncertain significance (Jun 14, 2016)
20-62841141-C-T		Multiple Epiphyseal Dysplasia, Dominant	Uncertain significance (Jun 14, 2016)
20-62841981-G-C		not specified	Uncertain significance (May 23, 2023)
20-62842012-C-T		not specified	Likely benign (Aug 04, 2021)
20-62842042-G-A		not specified	Uncertain significance (Apr 24, 2023)
20-62857485-T-C		not specified	Uncertain significance (Sep 22, 2022)
20-62857522-C-T		not specified	Uncertain significance (Sep 17, 2021)
20-62857536-C-T		not specified	Uncertain significance (Aug 30, 2021)
20-62859377-C-G		not specified	Uncertain significance (Mar 11, 2022)
20-62859408-C-T		not specified	Uncertain significance (Dec 30, 2023)
20-62859482-C-A		not specified	Uncertain significance (May 30, 2022)
20-62859492-G-A		not specified	Uncertain significance (Jun 16, 2023)
20-62859507-G-C		not specified	Uncertain significance (Jun 20, 2024)
20-62859507-G-T		not specified	Uncertain significance (Dec 17, 2023)
20-62860174-G-C		not specified	Uncertain significance (May 02, 2024)
20-62860207-G-T		not specified	Uncertain significance (Feb 11, 2022)
20-62861034-C-T		not specified	Uncertain significance (Aug 02, 2022)
20-62861045-T-A		not specified	Uncertain significance (Jun 02, 2023)
20-62861049-G-A		not specified	Uncertain significance (May 26, 2023)
20-62861070-C-G		not specified	Uncertain significance (Mar 30, 2024)
20-62861072-G-A		not specified	Uncertain significance (Aug 28, 2023)
20-62861118-C-G		not specified	Uncertain significance (Jan 04, 2022)
20-62861129-G-T		not specified	Uncertain significance (May 05, 2023)
20-62861147-G-C		not specified	Uncertain significance (Aug 17, 2021)
20-62861184-C-A		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCFL5	protein_coding	protein_coding	ENST00000335351	6	20649

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.991	0.00872	125739	0	3	125742	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	157	201	0.782	0.0000109	3165
Missense in Polyphen		58	93.485	0.62042		1245
Synonymous	-0.385	88	83.5	1.05	0.00000501	1064
Loss of Function	3.78	1	18.6	0.0537	0.00000112	216

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)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative transcription factor. Isoform 3 may play a role in early spermatogenesis. {ECO:0000269|PubMed:9763657}.

Haploinsufficiency Scores

• pHI: 0.0650
• hipred: Y
• hipred_score: 0.634
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.826

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcfl5

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;transcription by RNA polymerase II;multicellular organism development;spermatogenesis;cell differentiation;regulation of cell population proliferation;regulation of cell differentiation
• Cellular component: male germ cell nucleus;nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein dimerization activity