EMX1

empty spiracles homeobox 1, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 2:72916260-72936071

Links

ENSG00000135638 ∙ NCBI:2016 ∙ OMIM:600034 ∙ HGNC:3340 ∙ Uniprot:Q04741 ∙ 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 EMX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMX1 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			19
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	0	0

Variants in EMX1

This is a list of pathogenic ClinVar variants found in the EMX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-72917874-C-T		not specified	Uncertain significance (Jun 29, 2023)
2-72917892-C-G		not specified	Uncertain significance (Sep 14, 2022)
2-72917913-A-G		not specified	Uncertain significance (Mar 20, 2023)
2-72917917-C-T		not specified	Uncertain significance (Jul 26, 2022)
2-72917934-G-C		not specified	Uncertain significance (Jul 06, 2022)
2-72917935-C-T		not specified	Uncertain significance (Feb 12, 2025)
2-72917961-C-T		not specified	Uncertain significance (Feb 26, 2024)
2-72917967-G-A		not specified	Uncertain significance (Jan 20, 2023)
2-72918024-G-A		not specified	Uncertain significance (May 10, 2024)
2-72918025-G-A		not specified	Uncertain significance (Mar 03, 2025)
2-72918061-C-A		not specified	Uncertain significance (Aug 17, 2021)
2-72918129-G-C		not specified	Uncertain significance (Nov 11, 2024)
2-72918231-G-A		not specified	Uncertain significance (Oct 06, 2021)
2-72918241-T-A		not specified	Uncertain significance (Nov 26, 2024)
2-72918246-C-T		not specified	Uncertain significance (Sep 04, 2024)
2-72918283-C-A		not specified	Uncertain significance (Jul 30, 2024)
2-72918346-A-C		not specified	Uncertain significance (Dec 13, 2022)
2-72924356-C-T		not specified	Uncertain significance (Aug 17, 2022)
2-72924426-A-G		not specified	Uncertain significance (Nov 21, 2023)
2-72933932-T-C		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMX1	protein_coding	protein_coding	ENST00000258106	3	18632

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.895	0.104	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	82	137	0.598	0.00000706	1805
Missense in Polyphen		25	44.197	0.56564		549
Synonymous	-0.0329	60	59.7	1.01	0.00000300	618
Loss of Function	2.51	0	7.31	0.00	3.13e-7	91

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, which in cooperation with EMX2, acts to generate the boundary between the roof and archipallium in the developing brain. May function in combinations with OTX1/2 to specify cell fates in the developing central nervous system.

Recessive Scores

• pRec: 0.167

Haploinsufficiency Scores

• pHI: 0.338
• hipred: Y
• hipred_score: 0.626
• ghis: 0.652

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Emx1
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); craniofacial phenotype; skeleton phenotype; immune system phenotype; homeostasis/metabolism phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; neoplasm; hematopoietic 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); reproductive system 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); normal phenotype; vision/eye phenotype; hearing/vestibular/ear 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)

Zebrafish Information Network

• Gene name: emx1
• Affected structure: dorsal telencephalon
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: in utero embryonic development;regulation of transcription by RNA polymerase II;post-embryonic development;cerebral cortex regionalization;cerebral cortex neuron differentiation;response to drug;brain morphogenesis;homeostasis of number of cells;radial glial cell differentiation;neuroepithelial cell differentiation;regulation of oligodendrocyte progenitor proliferation;neuron projection extension
• Cellular component: nucleus;nucleolus;cytoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding