EBF1

EBF transcription factor 1, the group of Early B-cell factors|IPT domain containing

Basic information

Region (hg38): 5:158695915-159099916

Previous symbols: [ "EBF" ]

Links

ENSG00000164330 ∙ NCBI:1879 ∙ OMIM:164343 ∙ HGNC:3126 ∙ Uniprot:Q9UH73 ∙ 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 EBF1 gene.

• Inborn genetic diseases (11 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EBF1 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in EBF1

This is a list of pathogenic ClinVar variants found in the EBF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-158708011-G-T		not specified	Uncertain significance (Nov 12, 2021)
5-158708039-C-T		not specified	Uncertain significance (Oct 13, 2023)
5-158708078-C-T		not specified	Uncertain significance (Aug 17, 2022)
5-158712157-C-T		not specified	Uncertain significance (Apr 17, 2023)
5-158712255-G-C		not specified	Uncertain significance (Feb 05, 2024)
5-158712310-C-T		not specified	Uncertain significance (Jul 14, 2023)
5-158712975-T-C		not specified	Uncertain significance (Jan 11, 2023)
5-158712988-A-G		not specified	Uncertain significance (Nov 13, 2023)
5-158713033-C-T		not specified	Uncertain significance (Aug 08, 2022)
5-158713065-G-A		not specified	Uncertain significance (Nov 15, 2023)
5-158713074-G-A		not specified	Uncertain significance (Dec 16, 2023)
5-158713092-C-A		not specified	Uncertain significance (Nov 29, 2023)
5-158777461-T-G		not specified	Uncertain significance (Jun 16, 2023)
5-158796406-A-G		not specified	Uncertain significance (Jan 18, 2022)
5-158823286-C-T		not specified	Uncertain significance (Feb 28, 2023)
5-158840040-G-A			Uncertain significance (Jun 30, 2023)
5-159095633-G-T		not specified	Uncertain significance (Oct 10, 2023)
5-159095634-A-T		not specified	Uncertain significance (Oct 10, 2023)
5-159095666-G-A		not specified	Uncertain significance (May 22, 2023)
5-159099364-C-G		not specified	Uncertain significance (Jun 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EBF1	protein_coding	protein_coding	ENST00000313708	16	403842

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00303	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.38	184	366	0.503	0.0000214	3874
Missense in Polyphen		43	122.32	0.35154		1265
Synonymous	0.768	134	146	0.919	0.00000957	1153
Loss of Function	4.59	3	30.3	0.0991	0.00000145	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000184	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3'. {ECO:0000250}.
• Pathway: Transcriptional regulation of white adipocyte differentiation;White fat cell differentiation;Adipogenesis;Prion disease pathway;White fat cell differentiation (Consensus)

Recessive Scores

• pRec: 0.289

Intolerance Scores

• loftool: 0.124
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.990
• hipred: Y
• hipred_score: 0.824
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ebf1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; liver/biliary system phenotype; hematopoietic system 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular 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)

Gene ontology

• Biological process: multicellular organism development;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding;protein dimerization activity;C2H2 zinc finger domain binding