ELK4

ETS transcription factor ELK4, the group of ETS transcription factor family

Basic information

Region (hg38): 1:205597556-205632011

Links

ENSG00000158711 ∙ NCBI:2005 ∙ OMIM:600246 ∙ HGNC:3326 ∙ Uniprot:P28324 ∙ 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 ELK4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELK4 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in ELK4

This is a list of pathogenic ClinVar variants found in the ELK4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-205599173-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-205599225-A-G		not specified	Uncertain significance (Jun 18, 2021)
1-205616626-T-A		not specified	Uncertain significance (Aug 30, 2021)
1-205619003-G-A		not specified	Uncertain significance (Oct 21, 2024)
1-205619067-T-A		not specified	Uncertain significance (Apr 20, 2024)
1-205619997-G-A		not specified	Uncertain significance (Jul 12, 2023)
1-205620000-G-C		not specified	Uncertain significance (Sep 16, 2021)
1-205620007-A-G		not specified	Uncertain significance (Dec 19, 2022)
1-205620078-T-C		not specified	Uncertain significance (May 31, 2023)
1-205620081-G-C		not specified	Uncertain significance (Apr 19, 2023)
1-205620162-T-C		not specified	Uncertain significance (Sep 30, 2024)
1-205620176-C-T		not specified	Uncertain significance (Oct 08, 2024)
1-205620180-G-C		not specified	Uncertain significance (Jul 11, 2022)
1-205620187-A-G		not specified	Uncertain significance (Sep 06, 2022)
1-205620195-G-A		not specified	Uncertain significance (Sep 20, 2023)
1-205620268-G-T		not specified	Uncertain significance (Dec 07, 2021)
1-205620271-G-A		not specified	Likely benign (Aug 27, 2024)
1-205620307-T-C		not specified	Likely benign (May 27, 2022)
1-205620327-G-A		not specified	Uncertain significance (Sep 17, 2021)
1-205620402-G-C		not specified	Uncertain significance (Jan 03, 2024)
1-205620405-A-G		not specified	Uncertain significance (Aug 15, 2023)
1-205620406-T-C		not specified	Uncertain significance (May 01, 2024)
1-205620477-T-C		not specified	Uncertain significance (Jul 25, 2023)
1-205620523-G-T		not specified	Uncertain significance (Dec 02, 2024)
1-205620570-T-C		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELK4	protein_coding	protein_coding	ENST00000357992	4	24020

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00341	0.956	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.482	202	222	0.909	0.0000108	2805
Missense in Polyphen		54	81.212	0.66492		1017
Synonymous	-0.000434	86	86.0	1.00	0.00000425	906
Loss of Function	1.79	6	12.9	0.464	6.37e-7	176

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000886	0.0000879
Middle Eastern	0.0000548	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in both transcriptional activation and repression. Interaction with SIRT7 leads to recruitment and stabilization of SIRT7 at promoters, followed by deacetylation of histone H3 at 'Lys-18' (H3K18Ac) and subsequent transcription repression. Forms a ternary complex with the serum response factor (SRF). Requires DNA-bound SRF for ternary complex formation and makes extensive DNA contacts to the 5'side of SRF, but does not bind DNA autonomously. {ECO:0000269|PubMed:22722849}.
• Pathway: HTLV-I infection - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);EGF-Core;Mesodermal Commitment Pathway;MAPK Signaling Pathway;EGF-EGFR Signaling Pathway;ID signaling pathway;Serotonin HTR1 Group and FOS Pathway;Serotonin Receptor 2 and ELK-SRF-GATA4 signaling;Serotonin Receptor 4-6-7 and NR3C Signaling;FGF;PDGF;ID;Signaling mediated by p38-alpha and p38-beta (Consensus)

Recessive Scores

• pRec: 0.0959

Intolerance Scores

• loftool: 0.542
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.974
• hipred: Y
• hipred_score: 0.766
• ghis: 0.660

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: Elk4
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; vision/eye phenotype; immune system phenotype; homeostasis/metabolism phenotype; skeleton phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;cell differentiation;positive regulation of transcription by RNA polymerase II;histone H3 deacetylation
• Cellular component: nucleus;nucleoplasm;cytosol
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;core promoter binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;chromatin binding;DNA-binding transcription factor activity;transcription coregulator activity;protein binding