ELK1

ETS transcription factor ELK1, the group of ETS transcription factor family

Basic information

Region (hg38): X:47635520-47650604

Links

ENSG00000126767 ∙ NCBI:2002 ∙ OMIM:311040 ∙ HGNC:3321 ∙ Uniprot:P19419 ∙ 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 ELK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELK1 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				4	2	6
missense			9		4	13
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	4	6

Variants in ELK1

This is a list of pathogenic ClinVar variants found in the ELK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-47636862-G-A			Benign (May 21, 2018)
X-47637043-C-T			Benign (Dec 28, 2017)
X-47637796-A-G			Likely benign (Jun 01, 2022)
X-47637806-C-G		not specified	Uncertain significance (Dec 26, 2023)
X-47637844-C-T			Likely benign (Jun 08, 2018)
X-47637846-G-A		not specified	Uncertain significance (Jun 10, 2024)
X-47638007-G-A		not specified	Uncertain significance (Jul 25, 2023)
X-47638057-CG-C			Uncertain significance (Nov 01, 2018)
X-47638062-C-A			not provided (-)
X-47638076-T-G		not specified	Uncertain significance (Mar 30, 2024)
X-47638165-G-T			Benign (Dec 31, 2019)
X-47638907-G-A			Likely benign (Jan 01, 2023)
X-47638909-C-T		not specified	Uncertain significance (Mar 20, 2023)
X-47638921-C-A		not specified	Uncertain significance (Jun 30, 2022)
X-47638973-G-C			Likely benign (Apr 01, 2022)
X-47639001-C-T			Benign (Jan 04, 2022)
X-47639011-C-T		not specified	Uncertain significance (Mar 20, 2023)
X-47639035-G-C			Benign (Dec 28, 2017)
X-47639043-G-A		not specified	Uncertain significance (Dec 28, 2022)
X-47639077-G-A		not specified	Uncertain significance (Aug 08, 2022)
X-47639119-C-T			Benign (Dec 31, 2019)
X-47639142-C-A		not specified	Uncertain significance (Oct 10, 2023)
X-47639188-C-T		not specified	Uncertain significance (Jun 05, 2024)
X-47639192-T-C		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELK1	protein_coding	protein_coding	ENST00000247161	5	15084

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.937	0.0626	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.19	104	189	0.551	0.0000162	2684
Missense in Polyphen		29	92.106	0.31486		1428
Synonymous	0.656	81	88.9	0.911	0.00000808	967
Loss of Function	2.75	0	8.78	0.00	5.55e-7	160

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)	0.00	0.00
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 binds to purine-rich DNA sequences. Forms a ternary complex with SRF and the ETS and SRF motifs of the serum response element (SRE) on the promoter region of immediate early genes such as FOS and IER2. Induces target gene transcription upon JNK-signaling pathway stimulation (By similarity). {ECO:0000250|UniProtKB:A4GTP4, ECO:0000269|PubMed:1630903, ECO:0000269|PubMed:7889942}.
• Pathway: Prion diseases - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);GnRH signaling pathway - Homo sapiens (human);ErbB signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Endometrial cancer - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);EGFR Inhibitor Pathway, Pharmacodynamics;Intracellular Signalling Through Adenosine Receptor A2b and Adenosine;Intracellular Signalling Through Adenosine Receptor A2a and Adenosine;EGF-Core;IL-5 Signaling Pathway;SRF and miRs in Smooth Muscle Differentiation and Proliferation;Angiogenesis overview;Leptin signaling pathway;Prolactin Signaling Pathway;Androgen Receptor Network in Prostate Cancer;B Cell Receptor Signaling Pathway;Corticotropin-releasing hormone signaling pathway;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;JAK-STAT;Structural Pathway of Interleukin 1 (IL-1);nerve growth factor pathway (ngf);Focal Adhesion;Signaling of Hepatocyte Growth Factor Receptor;Photodynamic therapy-induced AP-1 survival signaling.;Association Between Physico-Chemical Features and Toxicity Associated Pathways;MAPK Signaling Pathway;ERK Pathway in Huntington,s Disease;IL-4 Signaling Pathway;VEGFA-VEGFR2 Signaling Pathway;ESC Pluripotency Pathways;PDGFR-beta pathway;Prion disease pathway;p38 MAPK Signaling Pathway;Endometrial cancer;MAPK Cascade;Ras Signaling;EGF-EGFR Signaling Pathway;Insulin Signaling;ID signaling pathway;ErbB Signaling Pathway;Estrogen signaling pathway;Serotonin HTR1 Group and FOS Pathway;Serotonin Receptor 2 and ELK-SRF-GATA4 signaling;Serotonin Receptor 4-6-7 and NR3C Signaling;Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Signal Transduction;Signaling by Interleukins;egf signaling pathway;p38 mapk signaling pathway;angiotensin ii mediated activation of jnk pathway via pyk2 dependent signaling;signaling pathway from g-protein families;t cell receptor signaling pathway;bcr signaling pathway;erk1/erk2 mapk signaling pathway;toll-like receptor pathway;mapkinase signaling pathway;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;igf-1 signaling pathway;HGF;HIF-2-alpha transcription factor network;IGF signaling;Innate Immune System;Immune System;Ghrelin;FGF;insulin Mam;Nuclear Events (kinase and transcription factor activation);BCR;pdgf signaling pathway;tpo signaling pathway;Signaling by NTRK1 (TRKA);fc epsilon receptor i signaling in mast cells;Signaling by NTRKs;BDNF;ERK/MAPK targets;EGFR1;MAPK targets/ Nuclear events mediated by MAP kinases;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;Ras signaling in the CD4+ TCR pathway;ErbB1 downstream signaling;fmlp induced chemokine gene expression in hmc-1 cells;MyD88 dependent cascade initiated on endosome;BCR signaling pathway;PDGF;IL2;NGF;Angiopoietin receptor Tie2-mediated signaling;IL4;IL5;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Signaling by Receptor Tyrosine Kinases;VEGF;ID;EGF;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Downstream signaling in naïve CD8+ T cells;PDGFR-beta signaling pathway;Trk receptor signaling mediated by the MAPK pathway;PDGFR-alpha signaling pathway;S1P2 pathway;insulin (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.27

Haploinsufficiency Scores

• pHI: 1.00
• hipred: Y
• hipred_score: 0.644
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.953

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elk1
• Phenotype: hematopoietic system phenotype; reproductive system phenotype; immune system phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;response to light stimulus;cell differentiation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;cellular response to testosterone stimulus;cellular response to gamma radiation;response to fibroblast growth factor;positive regulation of neuron death
• Cellular component: nucleus;nucleoplasm;mitochondrion;dendrite;neuronal cell body;axon terminus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II transcription factor binding;DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding;DNA-binding transcription factor activity;protein binding