EMILIN2

elastin microfibril interfacer 2, the group of EMI domain containing|C1q domain containing

Basic information

Region (hg38): 18:2847005-2916003

Links

ENSG00000132205 ∙ NCBI:84034 ∙ OMIM:608928 ∙ HGNC:19881 ∙ Uniprot:Q9BXX0 ∙ 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 EMILIN2 gene.

• Inborn genetic diseases (70 variants)
• not provided (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMILIN2 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				6	9	15
missense			66	5	5	76
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	66	11	15

Variants in EMILIN2

This is a list of pathogenic ClinVar variants found in the EMILIN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-2847292-G-C		not specified	Uncertain significance (Feb 10, 2022)
18-2847303-C-T		not specified	Uncertain significance (Sep 12, 2023)
18-2847860-G-C		not specified	Uncertain significance (May 06, 2022)
18-2847891-A-G		not specified	Uncertain significance (Sep 14, 2022)
18-2885038-C-T		not specified	Uncertain significance (May 23, 2023)
18-2885112-C-T			Benign (Dec 31, 2019)
18-2885136-A-C		not specified	Uncertain significance (Dec 03, 2021)
18-2890698-G-T		not specified	Uncertain significance (Jan 17, 2023)
18-2890705-G-A		not specified	Uncertain significance (Nov 16, 2021)
18-2890718-G-A			Benign (May 19, 2018)
18-2890735-C-T		not specified	Uncertain significance (Dec 20, 2023)
18-2890756-A-G		not specified	Uncertain significance (Oct 26, 2021)
18-2890770-G-A			Benign (Dec 31, 2019)
18-2890820-G-A			Likely benign (Nov 27, 2017)
18-2890855-C-A			Benign (Dec 31, 2019)
18-2890861-C-T		not specified	Uncertain significance (Feb 23, 2023)
18-2890902-A-G			Benign (Dec 31, 2019)
18-2890998-G-A		not specified	Uncertain significance (Sep 28, 2022)
18-2891041-C-T		not specified	Uncertain significance (Aug 15, 2023)
18-2891077-A-G		not specified	Uncertain significance (Feb 27, 2024)
18-2891097-G-A		not specified	Uncertain significance (Aug 04, 2021)
18-2891168-G-A			Benign (Jan 01, 2024)
18-2891191-G-A		not specified	Uncertain significance (Mar 02, 2023)
18-2891206-G-A		not specified	Uncertain significance (Dec 23, 2023)
18-2891217-G-A		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMILIN2	protein_coding	protein_coding	ENST00000254528	8	68964

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.62e-14	0.319	125596	0	152	125748	0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.271	518	536	0.967	0.0000300	6832
Missense in Polyphen		203	213.37	0.95138		2689
Synonymous	-0.215	226	222	1.02	0.0000141	2117
Loss of Function	1.32	26	34.3	0.757	0.00000173	445

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000803	0.000802
Ashkenazi Jewish	0.00318	0.00318
East Asian	0.000925	0.000925
Finnish	0.00105	0.000971
European (Non-Finnish)	0.000375	0.000369
Middle Eastern	0.000925	0.000925
South Asian	0.000230	0.000229
Other	0.00183	0.00179

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: 0.101

Intolerance Scores

• loftool: 0.901
• rvis_EVS: -0.5
• rvis_percentile_EVS: 21.86

Haploinsufficiency Scores

• pHI: 0.265
• hipred: N
• hipred_score: 0.146
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.603

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Emilin2
• Phenotype: hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: cell adhesion;biological_process;positive regulation of cell-substrate adhesion
• Cellular component: extracellular region;collagen trimer;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: protein binding;extracellular matrix constituent conferring elasticity