EOMES

eomesodermin, the group of T-box transcription factors

Basic information

Region (hg38): 3:27715949-27722711

Links

ENSG00000163508 ∙ NCBI:8320 ∙ OMIM:604615 ∙ HGNC:3372 ∙ Uniprot:O95936 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• microcephaly-polymicrogyria-corpus callosum agenesis syndrome (Supportive), mode of inheritance: AR
• microcephaly-polymicrogyria-corpus callosum agenesis syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EOMES gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EOMES 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	5	1	7
missense			52	2	1	55
nonsense						0
start loss						0
frameshift						0
inframe indel				2	1	3
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	9	3

Variants in EOMES

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

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

Position	Type	Phenotype	Significance	ClinVar
3-27717093-A-G		not specified	Uncertain significance (Jun 07, 2023)
3-27717105-T-A		not specified	Uncertain significance (Sep 22, 2023)
3-27717221-G-A		not specified	Uncertain significance (Sep 27, 2024)
3-27717239-T-C		not specified	Uncertain significance (Feb 08, 2025)
3-27717265-G-A		not specified	Benign (Jan 28, 2014)
3-27717319-C-G		not specified	Uncertain significance (Jun 30, 2024)
3-27717347-G-C		not specified	Uncertain significance (Oct 17, 2023)
3-27717427-G-A		not specified	Likely benign (Mar 09, 2017)
3-27717506-G-C		not specified	Uncertain significance (Apr 26, 2024)
3-27717576-G-A		not specified	Uncertain significance (Dec 21, 2022)
3-27717591-G-A		not specified	Uncertain significance (Jun 18, 2021)
3-27717645-C-T		not specified	Uncertain significance (Oct 19, 2024)
3-27717668-C-T		not specified	Uncertain significance (Feb 27, 2023)
3-27717701-G-C		not specified	Uncertain significance (Aug 05, 2024)
3-27717711-A-G		not specified	Uncertain significance (Apr 22, 2024)
3-27717720-C-T		not specified	Uncertain significance (Mar 09, 2025)
3-27717740-A-G		not specified	Uncertain significance (Dec 15, 2022)
3-27718797-T-A		not specified	Uncertain significance (Jun 13, 2022)
3-27718871-T-C		not specified	Uncertain significance (Aug 26, 2024)
3-27718876-G-A			Likely benign (Mar 01, 2024)
3-27719435-G-C		not specified	Uncertain significance (Nov 09, 2024)
3-27720174-G-T		not specified	Uncertain significance (Jun 05, 2024)
3-27720175-C-A		not specified	Uncertain significance (Jun 07, 2024)
3-27720258-C-T		not specified	Uncertain significance (Sep 30, 2024)
3-27720303-A-G		not specified	Uncertain significance (Aug 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EOMES	protein_coding	protein_coding	ENST00000295743	6	6767

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0156	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.861	303	348	0.870	0.0000177	4363
Missense in Polyphen		98	150.55	0.65094		1821
Synonymous	-1.09	163	146	1.12	0.00000790	1427
Loss of Function	4.17	3	25.9	0.116	0.00000141	289

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000334	0.000334
Middle Eastern	0.000109	0.000109
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a transcriptional activator playing a crucial role during development. Functions in trophoblast differentiation and later in gastrulation, regulating both mesoderm delamination and endoderm specification. Plays a role in brain development being required for the specification and the proliferation of the intermediate progenitor cells and their progeny in the cerebral cortex. Also involved in the differentiation of CD8+ T-cells during immune response regulating the expression of lytic effector genes. {ECO:0000269|PubMed:17353897, ECO:0000269|PubMed:17566017}.
• Disease: DISEASE: Note=A translocation t(3;10)(p24;q23) located 215 kb 3' to the EOMES gene but leading to loss of its expression was identified in a large consanguineous family. Homozygous silencing produces microcephaly associated with corpus callosum agenesis, bilateral polymicrogyria, ventricular dilatation and a small cerebellum.
• Pathway: Endoderm Differentiation;Mesodermal Commitment Pathway;POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation;Olfactory bulb development and olfactory learning;Development and heterogeneity of the ILC family;Developmental Biology;POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation;Transcriptional regulation of pluripotent stem cells;Downstream signaling in naïve CD8+ T cells;IL12-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.330

Haploinsufficiency Scores

• pHI: 0.485
• hipred: Y
• hipred_score: 0.789
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.633

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eomes
• Phenotype: neoplasm; hematopoietic system phenotype; normal phenotype; 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: eomesa
• Affected structure: blastodisc
• Phenotype tag: abnormal
• Phenotype quality: crowded

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;endoderm formation;mesoderm formation;endodermal cell fate specification;trophectodermal cell differentiation;adaptive immune response;CD8-positive, alpha-beta T cell differentiation involved in immune response;brain development;cardioblast differentiation;stem cell population maintenance;olfactory bulb development;cerebral cortex regionalization;cerebral cortex neuron differentiation;interferon-gamma production;skeletal muscle cell differentiation;negative regulation of DNA-binding transcription factor activity;positive regulation of cell differentiation;regulation of neuron differentiation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;cell differentiation involved in embryonic placenta development;mesodermal to mesenchymal transition involved in gastrulation
• Cellular component: nuclear chromatin
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II activating transcription factor binding;DNA binding;chromatin binding;sequence-specific DNA binding