EBF2

EBF transcription factor 2, the group of Early B-cell factors|IPT domain containing

Basic information

Region (hg38): 8:25841725-26045413

Links

ENSG00000221818 ∙ NCBI:64641 ∙ OMIM:609934 ∙ HGNC:19090 ∙ Uniprot:Q9HAK2 ∙ 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 EBF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EBF2 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	19	0	1

Variants in EBF2

This is a list of pathogenic ClinVar variants found in the EBF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-25844626-C-T		not specified	Uncertain significance (Mar 25, 2024)
8-25850605-T-C		not specified	Uncertain significance (May 18, 2023)
8-25850714-G-A		not specified	Uncertain significance (Dec 21, 2022)
8-25858342-G-A		not specified	Uncertain significance (May 26, 2022)
8-25858372-A-G		not specified	Uncertain significance (Jun 11, 2024)
8-25858411-A-G		not specified	Uncertain significance (Jun 17, 2024)
8-25858418-T-G		not specified	Uncertain significance (Oct 05, 2023)
8-25858472-G-A		not specified	Uncertain significance (Aug 02, 2021)
8-25861109-T-G		not specified	Uncertain significance (Oct 10, 2023)
8-25861133-C-T		not specified	Uncertain significance (May 24, 2023)
8-25861180-C-T		not specified	Uncertain significance (Oct 13, 2023)
8-25861305-T-C			Benign (Dec 31, 2019)
8-25862751-C-T			Benign (May 21, 2018)
8-25862773-T-C		not specified	Uncertain significance (Dec 07, 2022)
8-25886827-C-T		not specified	Uncertain significance (Jan 26, 2023)
8-25886845-G-C		not specified	Uncertain significance (Mar 16, 2024)
8-25889856-G-T		not specified	Uncertain significance (Mar 24, 2023)
8-26040038-C-T		not specified	Uncertain significance (Dec 20, 2023)
8-26040998-T-A		not specified	Uncertain significance (Mar 31, 2023)
8-26042166-G-C		not specified	Uncertain significance (Aug 02, 2021)
8-26042205-T-C		not specified	Uncertain significance (May 16, 2024)
8-26044749-G-T		not specified	Uncertain significance (Mar 18, 2024)
8-26044751-C-T		not specified	Uncertain significance (Feb 10, 2023)
8-26044804-A-C		not specified	Uncertain significance (Feb 27, 2023)
8-26044807-G-A		not specified	Uncertain significance (Jan 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EBF2	protein_coding	protein_coding	ENST00000520164	16	203668

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000240	124893	0	3	124896	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	221	329	0.672	0.0000168	3747
Missense in Polyphen		87	162.32	0.53599		1851
Synonymous	-0.435	136	130	1.05	0.00000736	1120
Loss of Function	4.97	2	32.6	0.0613	0.00000162	377

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000459	0.0000459
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that, in osteoblasts, activates the decoy receptor for RANKL, TNFRSF11B, which in turn regulates osteoclast differentiation. Acts in synergy with the Wnt- responsive LEF1/CTNNB1 pathway. Recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.332
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.16

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.837
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.682

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ebf2
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); taste/olfaction phenotype; cellular phenotype; craniofacial phenotype; reproductive system phenotype; 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); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail 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)

Gene ontology

• Biological process: cell fate determination;positive regulation of chromatin binding;positive regulation of transcription by RNA polymerase II;brown fat cell differentiation;adipose tissue development;positive regulation of cold-induced thermogenesis
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;metal ion binding;protein dimerization activity