ELK3

ETS transcription factor ELK3, the group of ETS transcription factor family

Basic information

Region (hg38): 12:96194374-96269824

Links

ENSG00000111145 ∙ NCBI:2004 ∙ OMIM:600247 ∙ HGNC:3325 ∙ Uniprot:P41970 ∙ 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 ELK3 gene.

• Inborn genetic diseases (11 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELK3 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			11	2		13
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	11	2	2

Variants in ELK3

This is a list of pathogenic ClinVar variants found in the ELK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-96223577-C-T		not specified	Uncertain significance (Oct 03, 2022)
12-96247002-C-G		not specified	Uncertain significance (Aug 02, 2021)
12-96247037-G-A		not specified	Uncertain significance (Mar 02, 2023)
12-96247063-G-A		not specified	Uncertain significance (Dec 21, 2022)
12-96247079-C-T		not specified	Uncertain significance (Jan 08, 2024)
12-96247252-C-G		not specified	Uncertain significance (Oct 05, 2023)
12-96247252-C-T		not specified	Uncertain significance (Oct 10, 2023)
12-96247334-T-C		not specified	Uncertain significance (Dec 27, 2022)
12-96247340-C-T		not specified	Uncertain significance (Feb 28, 2024)
12-96247343-C-T			Likely benign (May 04, 2018)
12-96247384-G-C		not specified	Uncertain significance (Sep 14, 2023)
12-96247399-T-G		not specified	Uncertain significance (Jul 13, 2022)
12-96247410-G-A			Likely benign (Jun 06, 2018)
12-96247541-C-T		not specified	Uncertain significance (Aug 17, 2021)
12-96247566-G-A			Benign (Jul 11, 2018)
12-96247640-C-T		not specified	Uncertain significance (Dec 27, 2023)
12-96247654-G-A		not specified	Uncertain significance (Dec 06, 2021)
12-96247658-C-T		not specified	Uncertain significance (Dec 09, 2023)
12-96247726-A-G		not specified	Uncertain significance (Mar 06, 2023)
12-96259757-G-A			Benign (Jun 29, 2018)
12-96259821-G-A		not specified	Uncertain significance (Aug 26, 2022)
12-96259843-C-T		not specified	Uncertain significance (Dec 22, 2023)
12-96259860-G-A			Benign (Jun 06, 2018)
12-96267099-T-G		not specified	Uncertain significance (Feb 28, 2023)
12-96267105-C-A		not specified	Uncertain significance (Nov 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELK3	protein_coding	protein_coding	ENST00000228741	4	75454

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0835	0.908	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.580	214	239	0.894	0.0000151	2606
Missense in Polyphen		65	91.396	0.71119		1059
Synonymous	-2.20	151	120	1.26	0.00000937	880
Loss of Function	2.28	4	12.8	0.312	7.18e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000213
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.000231	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a negative regulator of transcription, but can activate transcription when coexpressed with Ras, Src or Mos. Forms a ternary complex with the serum response factor and the ETS and SRF motifs of the Fos serum response element.
• Pathway: EGF-Core;ID signaling pathway;FGF;ID (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.499
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.54

Haploinsufficiency Scores

• pHI: 0.997
• hipred: Y
• hipred_score: 0.705
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elk3
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); vision/eye phenotype; immune system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;angiogenesis;regulation of transcription by RNA polymerase II;signal transduction;cell differentiation;wound healing;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;mitochondrion
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;purine-rich negative regulatory element binding