ELF1

E74 like ETS transcription factor 1, the group of ETS transcription factor family

Basic information

Region (hg38): 13:40931923-41061440

Links

ENSG00000120690 ∙ NCBI:1997 ∙ OMIM:189973 ∙ HGNC:3316 ∙ Uniprot:P32519 ∙ 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 ELF1 gene.

• Inborn genetic diseases (26 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELF1 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	2

Variants in ELF1

This is a list of pathogenic ClinVar variants found in the ELF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-40933443-C-T			Benign (Sep 11, 2018)
13-40933447-A-T		not specified	Uncertain significance (May 03, 2023)
13-40933449-T-A		not specified	Uncertain significance (May 24, 2023)
13-40933450-T-G		not specified	Uncertain significance (May 24, 2023)
13-40933519-G-A		not specified	Uncertain significance (Oct 17, 2023)
13-40933528-T-C		not specified	Uncertain significance (Feb 27, 2023)
13-40933633-G-A		not specified	Uncertain significance (Jun 29, 2022)
13-40933636-C-T		not specified	Uncertain significance (Nov 09, 2021)
13-40933688-G-A		not specified	Uncertain significance (Jun 07, 2023)
13-40933727-C-T		not specified	Uncertain significance (Feb 06, 2023)
13-40933753-T-C		not specified	Uncertain significance (May 03, 2023)
13-40933759-G-T		not specified	Uncertain significance (May 25, 2022)
13-40933890-C-A		not specified	Uncertain significance (Oct 13, 2023)
13-40933988-G-A		not specified	Uncertain significance (Feb 17, 2022)
13-40941021-C-G		not specified	Uncertain significance (Dec 28, 2023)
13-40941053-T-A		not specified	Uncertain significance (Nov 21, 2023)
13-40941066-C-T		not specified	Uncertain significance (Jan 10, 2023)
13-40941071-C-T		not specified	Uncertain significance (Mar 23, 2022)
13-40941085-T-A			Benign (Feb 12, 2018)
13-40941101-A-C		not specified	Uncertain significance (May 18, 2022)
13-40941137-G-A		not specified	Uncertain significance (Jul 14, 2021)
13-40941188-C-T		not specified	Uncertain significance (Nov 18, 2022)
13-40941209-C-G		not specified	Uncertain significance (Dec 22, 2023)
13-40941236-G-A		not specified	Uncertain significance (Jul 25, 2023)
13-40941240-G-A		not specified	Uncertain significance (Jan 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELF1	protein_coding	protein_coding	ENST00000239882	8	129521

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0106	0.989	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.914	279	325	0.857	0.0000165	4008
Missense in Polyphen		65	107.06	0.60713		1404
Synonymous	0.466	114	121	0.946	0.00000674	1245
Loss of Function	3.12	8	24.7	0.324	0.00000123	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000953	0.0000924
European (Non-Finnish)	0.0000970	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.0000665	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that activates the LYN and BLK promoters. Appears to be required for the T-cell-receptor-mediated trans activation of HIV-2 gene expression. Binds specifically to two purine-rich motifs in the HIV-2 enhancer. {ECO:0000269|PubMed:8756667}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;RUNX1 regulates transcription of genes involved in BCR signaling;Angiopoietin receptor Tie2-mediated signaling;RUNX1 regulates transcription of genes involved in interleukin signaling;Transcriptional regulation by RUNX1;IL2 signaling events mediated by STAT5;AP-1 transcription factor network;Regulation of retinoblastoma protein (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.501
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.71

Haploinsufficiency Scores

• pHI: 0.768
• hipred: Y
• hipred_score: 0.758
• ghis: 0.509

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	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Elf1
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: regulation of cytokine production;regulation of cytokine-mediated signaling pathway;regulation of transcription by RNA polymerase II;cell differentiation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;regulation of B cell receptor signaling pathway;negative regulation of T cell receptor signaling pathway
• Cellular component: nucleus;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;protein binding