EMILIN1

elastin microfibril interfacer 1, the group of EMI domain containing|C1q domain containing

Basic information

Region (hg38): 2:27078614-27086403

Links

ENSG00000138080 ∙ NCBI:11117 ∙ OMIM:130660 ∙ HGNC:19880 ∙ Uniprot:Q9Y6C2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neuronopathy, distal hereditary motor, autosomal dominant 10 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neuronopathy, distal hereditary motor, type X	AD	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	Musculoskeletal; Neurologic	26462740; 31978608

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EMILIN1 gene.

• Inborn genetic diseases (59 variants)
• not provided (13 variants)
• Arterial tortuosity (1 variants)
• EMILIN-1-related connective tissue disease (1 variants)
• EMILIN1-related condition (1 variants)
• Neuronopathy, distal hereditary motor, autosomal dominant 10 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMILIN1 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	1	3
missense			61	4	3	68
nonsense						0
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	1	0	61	6	4

Highest pathogenic variant AF is 0.0000197

Variants in EMILIN1

This is a list of pathogenic ClinVar variants found in the EMILIN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27079063-G-A		EMILIN1-related disorder	Benign (Dec 06, 2019)
2-27079072-C-A		Inborn genetic diseases	Uncertain significance (Oct 17, 2023)
2-27079075-C-G		Inborn genetic diseases	Uncertain significance (Jul 14, 2023)
2-27079112-C-T		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
2-27079129-G-A		Inborn genetic diseases • Neuronopathy, distal hereditary motor, autosomal dominant 10	Uncertain significance (May 29, 2013)
2-27079166-G-T		Inborn genetic diseases	Uncertain significance (Dec 22, 2023)
2-27079183-A-AG		Arterial tortuosity	Pathogenic (Feb 09, 2023)
2-27079210-GC-G		Arterial tortuosity	Pathogenic (-)
2-27079219-C-A		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
2-27079221-A-G			Likely benign (Feb 01, 2023)
2-27079228-C-A			Uncertain significance (Jan 22, 2024)
2-27080147-A-G		EMILIN1-related disorder	Likely benign (Dec 23, 2019)
2-27080167-G-A		Inborn genetic diseases	Uncertain significance (Jul 20, 2022)
2-27080177-G-A		Malignant tumor of prostate	Uncertain significance (-)
2-27080194-C-G		EMILIN1-related disorder	Benign (Jan 07, 2020)
2-27080255-G-A		Inborn genetic diseases	Uncertain significance (Mar 01, 2023)
2-27080793-T-G		Inborn genetic diseases	Uncertain significance (Aug 08, 2023)
2-27080817-G-A		Inborn genetic diseases	Uncertain significance (Aug 30, 2021)
2-27080848-C-T		Inborn genetic diseases	Uncertain significance (Aug 15, 2023)
2-27080872-C-T		Inborn genetic diseases	Uncertain significance (May 27, 2022)
2-27080875-G-A		Inborn genetic diseases	Uncertain significance (Apr 13, 2023)
2-27080881-T-C		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)
2-27080896-G-A		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
2-27080902-A-G		Inborn genetic diseases	Uncertain significance (Jun 26, 2023)
2-27080937-G-C		Inborn genetic diseases	Uncertain significance (Jul 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMILIN1	protein_coding	protein_coding	ENST00000380320	8	7837

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00439	0.996	125684	0	64	125748	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	526	610	0.862	0.0000389	6307
Missense in Polyphen		185	235.83	0.78447		2513
Synonymous	1.12	243	266	0.913	0.0000154	2307
Loss of Function	3.82	11	35.6	0.309	0.00000190	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000238	0.000237
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00158	0.00157
European (Non-Finnish)	0.000180	0.000167
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000994	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be responsible for anchoring smooth muscle cells to elastic fibers, and may be involved not only in the formation of the elastic fiber, but also in the processes that regulate vessel assembly. Has cell adhesive capacity.

Recessive Scores

• pRec: 0.148

Intolerance Scores

• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.57

Haploinsufficiency Scores

• pHI: 0.303
• hipred: N
• hipred_score: 0.432
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.621

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Emilin1
• 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); homeostasis/metabolism phenotype; 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)

Zebrafish Information Network

• Gene name: emilin1a
• Affected structure: thrombocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: aortic valve morphogenesis;cell adhesion;cell-matrix adhesion;positive regulation of gene expression;negative regulation of gene expression;positive regulation of cell-substrate adhesion;cell migration;negative regulation of angiogenesis;negative regulation of transforming growth factor beta receptor signaling pathway;negative regulation of vascular endothelial growth factor receptor signaling pathway;negative regulation of collagen biosynthetic process;elastic fiber assembly;negative regulation of cell activation;negative regulation of pathway-restricted SMAD protein phosphorylation;protein homotrimerization;negative regulation of ERK1 and ERK2 cascade;positive regulation of extracellular matrix assembly;negative regulation of collagen fibril organization;negative regulation of macrophage migration
• Cellular component: extracellular region;collagen trimer;extracellular space;extracellular matrix;integrin alpha4-beta1 complex;collagen-containing extracellular matrix;extracellular exosome;EMILIN complex
• Molecular function: protein binding;extracellular matrix constituent conferring elasticity;identical protein binding;integrin binding involved in cell-matrix adhesion