ELF2

E74 like ETS transcription factor 2, the group of ETS transcription factor family

Basic information

Region (hg38): 4:139028111-139177218

Links

ENSG00000109381 ∙ NCBI:1998 ∙ OMIM:619798 ∙ HGNC:3317 ∙ Uniprot:Q15723 ∙ 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 ELF2 gene.

• Inborn genetic diseases (11 variants)
• not provided (2 variants)
• Cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELF2 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		1	11			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	11	1	0

Variants in ELF2

This is a list of pathogenic ClinVar variants found in the ELF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-139043197-T-C		not specified	Uncertain significance (Dec 28, 2022)
4-139043230-C-T		not specified	Uncertain significance (Dec 01, 2022)
4-139043286-G-C		not specified	Uncertain significance (Nov 10, 2022)
4-139043288-T-C			Benign (May 29, 2018)
4-139044674-C-T		not specified	Uncertain significance (Jun 02, 2023)
4-139044725-A-G		not specified	Uncertain significance (Jan 03, 2024)
4-139044899-C-T		not specified	Uncertain significance (Jun 29, 2023)
4-139044907-C-T			Likely benign (Apr 04, 2018)
4-139044947-G-A		not specified	Uncertain significance (May 09, 2023)
4-139045020-G-T		not specified	Uncertain significance (Feb 27, 2024)
4-139045025-G-A		not specified	Uncertain significance (Oct 12, 2021)
4-139045281-C-T		not specified	Uncertain significance (Oct 17, 2023)
4-139045297-G-T		not specified	Uncertain significance (Oct 27, 2023)
4-139059036-T-C		not specified	Uncertain significance (Dec 16, 2022)
4-139059155-G-A		not specified	Uncertain significance (Oct 12, 2022)
4-139059224-G-A		not specified	Uncertain significance (Feb 27, 2023)
4-139059234-A-T		not specified	Uncertain significance (Jul 13, 2021)
4-139059370-T-C			Likely benign (Jan 01, 2023)
4-139059447-T-G		not specified	Uncertain significance (Dec 28, 2022)
4-139059579-C-G		not specified	Uncertain significance (Nov 09, 2023)
4-139059587-T-C		not specified	Uncertain significance (Dec 27, 2023)
4-139060333-G-A		not specified	Uncertain significance (Jun 21, 2022)
4-139060496-T-C		not specified	Uncertain significance (Dec 20, 2023)
4-139067770-A-G		not specified	Uncertain significance (Oct 10, 2023)
4-139071977-C-T		not specified	Uncertain significance (Dec 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELF2	protein_coding	protein_coding	ENST00000394235	8	149107

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00518	125740	0	6	125746	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	228	306	0.744	0.0000143	3739
Missense in Polyphen		67	119.25	0.56186		1495
Synonymous	0.771	98	108	0.906	0.00000526	1197
Loss of Function	4.20	2	24.4	0.0819	0.00000127	314

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000359	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1 transcriptionally activates the LYN and BLK promoters and acts synergistically with RUNX1 to transactivate the BLK promoter.
• Pathway: Beta-agonist/Beta-blocker Pathway, Pharmacodynamics;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;RUNX1 regulates transcription of genes involved in BCR signaling;Angiopoietin receptor Tie2-mediated signaling;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.0855
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.82

Haploinsufficiency Scores

• pHI: 0.195
• hipred: Y
• hipred_score: 0.654
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.985

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elf2

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cell differentiation;positive regulation of transcription, DNA-templated;regulation of B cell receptor signaling pathway
• Cellular component: nucleus;nucleoplasm;cytosol;nuclear body
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding