EML1

EMAP like 1, the group of EMAP like|WD repeat domain containing

Basic information

Region (hg38): 14:99737692-99942060

Previous symbols: [ "EMAPL" ]

Links

ENSG00000066629 ∙ NCBI:2009 ∙ OMIM:602033 ∙ HGNC:3330 ∙ Uniprot:O00423 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• band heterotopia of brain (Strong), mode of inheritance: AR
• band heterotopia of brain (Strong), mode of inheritance: AR
• subcortical band heterotopia (Supportive), mode of inheritance: AR
• band heterotopia of brain (Moderate), mode of inheritance: AR
• band heterotopia of brain (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Band heterotopia	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	24859200

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EML1 gene.

• not provided (109 variants)
• Inborn genetic diseases (22 variants)
• Band heterotopia of brain (7 variants)
• not specified (1 variants)
• EML1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EML1 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	31	8	40
missense			32	2	3	37
nonsense		2	1			3
start loss						0
frameshift	2					2
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1					1
splice region				4	2	6
non coding				6	37	43
Total	3	2	35	39	48

Variants in EML1

This is a list of pathogenic ClinVar variants found in the EML1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-99850861-G-A		Inborn genetic diseases	Uncertain significance (Dec 18, 2023)
14-99850906-C-G		Inborn genetic diseases	Uncertain significance (May 18, 2023)
14-99850921-C-T		Band heterotopia of brain	Likely pathogenic (Aug 24, 2022)
14-99850924-A-C		Inborn genetic diseases	Uncertain significance (Dec 15, 2022)
14-99850935-C-T			Benign (Jan 26, 2024)
14-99850936-G-A		Inborn genetic diseases	Uncertain significance (Aug 17, 2022)
14-99850958-C-G		Inborn genetic diseases	Uncertain significance (Jul 26, 2022)
14-99850980-G-A			Likely benign (Nov 27, 2023)
14-99850992-T-C			Likely benign (Oct 01, 2023)
14-99851007-C-T			Likely benign (Aug 09, 2023)
14-99851039-G-A			Benign (Jan 29, 2024)
14-99851041-C-T		EML1-related disorder	Likely benign (Feb 20, 2019)
14-99851135-G-A			Benign (May 11, 2021)
14-99865318-G-A			Benign (May 11, 2021)
14-99865506-T-C			Likely benign (Jun 27, 2023)
14-99865516-A-C		EML1-related disorder	Likely benign (Mar 08, 2019)
14-99865539-T-C		Band heterotopia of brain	Benign (Jan 29, 2024)
14-99865551-G-A			Likely benign (Apr 13, 2018)
14-99865556-A-G		Inborn genetic diseases	Uncertain significance (Dec 05, 2022)
14-99865589-G-A			Benign (Dec 07, 2023)
14-99865603-C-G			Uncertain significance (Jul 23, 2022)
14-99865608-C-T			Benign (Aug 04, 2023)
14-99865619-A-G		Inborn genetic diseases • EML1-related disorder	Conflicting classifications of pathogenicity (Jan 02, 2024)
14-99865657-A-G			Likely benign (Jan 09, 2023)
14-99875093-A-G			Benign (May 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EML1	protein_coding	protein_coding	ENST00000334192	23	204368

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00392	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.45	326	477	0.684	0.0000278	5435
Missense in Polyphen		108	197.28	0.54744		2169
Synonymous	0.736	176	189	0.932	0.0000126	1639
Loss of Function	5.63	8	51.6	0.155	0.00000289	571

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00127	0.00126
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Modulates the assembly and organization of the microtubule cytoskeleton, and probably plays a role in regulating the orientation of the mitotic spindle and the orientation of the plane of cell division. Required for normal proliferation of neuronal progenitor cells in the developing brain and for normal brain development. Does not affect neuron migration per se. {ECO:0000250|UniProtKB:Q05BC3}.
• Disease: DISEASE: Band heterotopia (BH) [MIM:600348]: A brain malformation of the lissencephaly spectrum, resulting from disordered neuronal migration and characterized by bands of gray matter interposed in the central white matter. Disease features include severe developmental delay with intellectual disability, enlarged head circumference, periventricular and ribbon-like subcortical heterotopia, polymicrogyria and agenesis of the corpus callosum. {ECO:0000269|PubMed:24859200}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.164

Intolerance Scores

• loftool: 0.419
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.73

Haploinsufficiency Scores

• pHI: 0.291
• hipred: Y
• hipred_score: 0.728
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.564

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eml1
• 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); vision/eye phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); muscle phenotype; craniofacial phenotype; cellular 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); growth/size/body region phenotype

Zebrafish Information Network

• Gene name: eml1
• Affected structure: retinal cone cell
• Phenotype tag: abnormal
• Phenotype quality: photosensitive

Gene ontology

• Biological process: microtubule cytoskeleton organization;hematopoietic progenitor cell differentiation;mitotic spindle organization;neuroblast proliferation;brain development
• Cellular component: cytosol;microtubule;microtubule associated complex;microtubule cytoskeleton;perinuclear region of cytoplasm;mitotic spindle pole;mitotic spindle midzone
• Molecular function: calcium ion binding;protein binding;microtubule binding;tubulin binding