EN2

engrailed homeobox 2, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 7:155458129-155464831

Links

ENSG00000164778

∙ NCBI:2020 ∙ OMIM:131310 ∙ HGNC:3343 ∙ Uniprot:P19622 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

complex neurodevelopmental disorder (Disputed Evidence), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EN2 gene.

not_specified (65 variants)
not_provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EN2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001427.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	3 clinvar	4
missense			64 clinvar	1 clinvar		65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	64	2	3

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EN2	protein_coding	protein_coding	ENST00000297375	2	6703

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.634	0.359	121986	0	1	121987	0.00000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	88	122	0.724	0.00000590	2054
Missense in Polyphen		31	48.778	0.63554		669
Synonymous	-0.232	58	55.8	1.04	0.00000269	698
Loss of Function	2.20	1	7.48	0.134	3.65e-7	107

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)	0.00000902	0.00000902
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Disease: DISEASE: Note=Genetic variations in EN2 may be associated with susceptibility to autism.;
Pathway: Dopaminergic Neurogenesis (Consensus)

Recessive Scores

pRec: 0.415

Haploinsufficiency Scores

pHI: 0.195
hipred: Y
hipred_score: 0.670
ghis: 0.472

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.885

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: En2
Phenotype: cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; embryo 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); digestive/alimentary 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);

Zebrafish Information Network

Gene name: en2a
Affected structure: optic tectum
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: multicellular organism development;midbrain development;hindbrain development;negative regulation of neuron apoptotic process;positive regulation of transcription by RNA polymerase II;neuron development;embryonic brain development
Cellular component: fibrillar center;nucleus;nucleolus;membrane
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding