ECM1

extracellular matrix protein 1

Basic information

Region (hg38): 1:150508062-150513789

Links

ENSG00000143369 ∙ NCBI:1893 ∙ OMIM:602201 ∙ HGNC:3153 ∙ Uniprot:Q16610 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• lipoid proteinosis (Definitive), mode of inheritance: AR
• lipoid proteinosis (Strong), mode of inheritance: AR
• lipoid proteinosis (Supportive), mode of inheritance: AR
• lipoid proteinosis (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Lipoid proteinosis	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	Audiologic/Otolaryngologic; Biochemical; Dermatologic; Neurologic; Pulmonary	5002423; 751090; 4087005; 11929856; 12603844; 19519837; 19734986; 21349189; 21791056; 21886756; 22182433

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ECM1 gene.

• Lipid proteinosis (9 variants)
• not provided (3 variants)
• ECM1-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ECM1 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				11	4	15
missense		2	37	6	5	50
nonsense	4	2				6
start loss						0
frameshift	4	4				8
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region			1		1	2
non coding			1	4	15	20
Total	9	8	38	21	24

Highest pathogenic variant AF is 0.0000197

Variants in ECM1

This is a list of pathogenic ClinVar variants found in the ECM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-150508095-G-A			Benign (Jul 09, 2018)
1-150508113-G-A			Benign (Jul 10, 2018)
1-150508228-G-A		Inborn genetic diseases	Uncertain significance (Jun 08, 2021)
1-150508255-GTTGC-G		Lipid proteinosis	Likely pathogenic (Sep 22, 2024)
1-150509262-C-T			Benign (Jul 09, 2018)
1-150509420-C-T			Benign (Jul 09, 2018)
1-150509506-C-T			Likely benign (Jul 06, 2018)
1-150509537-C-T		Inborn genetic diseases	Uncertain significance (May 01, 2022)
1-150509553-GC-TT		Lipid proteinosis	not provided (-)
1-150509578-G-A		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)
1-150509658-T-G		Lipid proteinosis	Uncertain significance (Dec 13, 2019)
1-150509668-C-T		ECM1-related disorder	Likely benign (Aug 03, 2020)
1-150509669-G-A		ECM1-related disorder	Benign (Dec 31, 2019)
1-150509675-C-G		Inborn genetic diseases	Uncertain significance (Feb 02, 2022)
1-150509680-CT-C		Lipid proteinosis	Likely pathogenic (Jan 22, 2019)
1-150509683-C-A			Likely benign (Dec 31, 2019)
1-150509685-C-A		ECM1-related disorder	Likely benign (May 25, 2022)
1-150509686-A-C			Likely benign (Jan 12, 2018)
1-150509696-C-T		Lipid proteinosis	Pathogenic (Mar 22, 2024)
1-150509779-A-G			Benign (Jul 09, 2018)
1-150509802-G-T			Likely benign (Jul 10, 2018)
1-150509830-T-C		Inborn genetic diseases	Uncertain significance (Oct 29, 2021)
1-150509926-GC-G		Lipid proteinosis • ECM1-related disorder	Pathogenic/Likely pathogenic (Apr 11, 2023)
1-150509927-C-T		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)
1-150509929-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ECM1	protein_coding	protein_coding	ENST00000369049	10	5728

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.66e-14	0.174	125647	0	101	125748	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.224	336	325	1.03	0.0000198	3684
Missense in Polyphen		118	115.23	1.024		1355
Synonymous	0.0945	121	122	0.989	0.00000628	1155
Loss of Function	1.01	24	30.0	0.801	0.00000192	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000572	0.000572
Ashkenazi Jewish	0.000700	0.000695
East Asian	0.000163	0.000163
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000612	0.000536
Middle Eastern	0.000163	0.000163
South Asian	0.000297	0.000294
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in endochondral bone formation as negative regulator of bone mineralization. Stimulates the proliferation of endothelial cells and promotes angiogenesis. Inhibits MMP9 proteolytic activity. {ECO:0000269|PubMed:11165938, ECO:0000269|PubMed:11292659, ECO:0000269|PubMed:16512877}.
• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.301

Intolerance Scores

• loftool: 0.427
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.82

Haploinsufficiency Scores

• pHI: 0.148
• hipred: N
• hipred_score: 0.173
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ecm1
• Phenotype: immune system 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); hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: ossification;angiogenesis;positive regulation of endothelial cell proliferation;negative regulation of cytokine-mediated signaling pathway;chondrocyte development;platelet degranulation;regulation of type 2 immune response;endochondral bone growth;regulation of transcription by RNA polymerase II;inflammatory response;signal transduction;negative regulation of peptidase activity;negative regulation of bone mineralization;biomineral tissue development;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of angiogenesis;regulation of T cell migration
• Cellular component: extracellular region;extracellular matrix;platelet dense granule lumen;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: protease binding;interleukin-2 receptor binding;extracellular matrix structural constituent;protein binding;protein C-terminus binding;enzyme binding;laminin binding