EMILIN3

elastin microfibril interfacer 3, the group of EMI domain containing

Basic information

Region (hg38): 20:41359962-41366818

Previous symbols: [ "C20orf130", "EMILIN5" ]

Links

ENSG00000183798 ∙ NCBI:90187 ∙ OMIM:608929 ∙ HGNC:16123 ∙ Uniprot:Q9NT22 ∙ 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 EMILIN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMILIN3 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		1
missense			54	4		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	5	0

Variants in EMILIN3

This is a list of pathogenic ClinVar variants found in the EMILIN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-41361276-C-T		not specified	Uncertain significance (Dec 08, 2023)
20-41361278-T-G		not specified	Uncertain significance (Mar 13, 2023)
20-41361287-C-T		not specified	Uncertain significance (Jan 26, 2022)
20-41361292-C-G		not specified	Uncertain significance (Apr 29, 2024)
20-41361330-C-G		not specified	Uncertain significance (Aug 01, 2022)
20-41361371-C-T		not specified	Uncertain significance (Feb 27, 2023)
20-41361372-G-A		not specified	Uncertain significance (Apr 05, 2023)
20-41361494-C-A		not specified	Uncertain significance (Apr 07, 2023)
20-41361494-C-T		not specified	Uncertain significance (Jun 05, 2023)
20-41361675-C-T		not specified	Uncertain significance (Sep 26, 2023)
20-41361684-C-T		not specified	Uncertain significance (Aug 02, 2021)
20-41361731-A-G			Likely benign (Feb 01, 2023)
20-41361851-G-A		not specified	Uncertain significance (Mar 11, 2024)
20-41361876-C-T		not specified	Uncertain significance (Aug 15, 2023)
20-41361884-T-C		not specified	Uncertain significance (Aug 29, 2023)
20-41361924-G-A		Marfanoid habitus and intellectual disability	Uncertain significance (-)
20-41361940-C-T			Likely benign (Feb 01, 2023)
20-41362070-C-T		not specified	Uncertain significance (Mar 17, 2023)
20-41362092-C-T		not specified	Likely benign (Jan 06, 2023)
20-41362130-C-T		not specified	Uncertain significance (Feb 23, 2023)
20-41362149-C-G		not specified	Uncertain significance (Jun 02, 2023)
20-41362151-C-T		not specified	Uncertain significance (May 04, 2022)
20-41362193-C-G		not specified	Uncertain significance (May 13, 2022)
20-41362197-T-A		not specified	Uncertain significance (Feb 28, 2024)
20-41362227-C-T		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMILIN3	protein_coding	protein_coding	ENST00000332312	4	6862

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000924	0.985	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.279	424	440	0.963	0.0000280	4803
Missense in Polyphen		124	127.09	0.97568		1373
Synonymous	0.428	180	187	0.960	0.0000112	1721
Loss of Function	2.20	12	23.5	0.510	0.00000128	259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000775	0.000768
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000137	0.0000924
European (Non-Finnish)	0.000241	0.000237
Middle Eastern	0.000218	0.000217
South Asian	0.000232	0.000229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0987

Intolerance Scores

• loftool: 0.725
• rvis_EVS: -0.59
• rvis_percentile_EVS: 18.26

Haploinsufficiency Scores

• pHI: 0.151
• hipred: N
• hipred_score: 0.322
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.567

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Emilin3

Gene ontology

• Biological process: positive regulation of cell-substrate adhesion
• Cellular component: cytoplasm;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: extracellular matrix constituent conferring elasticity