ECM2

extracellular matrix protein 2

Basic information

Region (hg38): 9:92493553-92536655

Links

ENSG00000106823 ∙ NCBI:1842 ∙ OMIM:603479 ∙ HGNC:3154 ∙ Uniprot:O94769 ∙ 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 ECM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ECM2 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						0
missense			41	2		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	2	0

Variants in ECM2

This is a list of pathogenic ClinVar variants found in the ECM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-92496379-G-A		not specified	Uncertain significance (Jan 23, 2023)
9-92500728-G-A		not specified	Uncertain significance (May 26, 2024)
9-92500760-A-C		not specified	Uncertain significance (Aug 08, 2022)
9-92500776-G-T		not specified	Uncertain significance (Apr 23, 2024)
9-92500847-T-C		not specified	Uncertain significance (Nov 17, 2022)
9-92500859-C-T		not specified	Uncertain significance (Sep 26, 2023)
9-92500873-A-T		not specified	Uncertain significance (Jun 24, 2022)
9-92500901-A-C		not specified	Uncertain significance (May 21, 2024)
9-92500950-G-A		not specified	Uncertain significance (Feb 23, 2023)
9-92501006-G-A		not specified	Uncertain significance (Mar 04, 2024)
9-92502558-T-C		not specified	Uncertain significance (Dec 02, 2022)
9-92502585-A-G		not specified	Uncertain significance (Aug 15, 2023)
9-92502596-A-T		not specified	Uncertain significance (Sep 16, 2021)
9-92502615-G-A		not specified	Uncertain significance (Nov 13, 2023)
9-92505537-A-G		not specified	Uncertain significance (Jan 23, 2023)
9-92505558-G-A		not specified	Uncertain significance (Feb 07, 2023)
9-92505585-A-G		not specified	Uncertain significance (Feb 11, 2022)
9-92505589-G-T		not specified	Uncertain significance (Jan 30, 2024)
9-92505600-A-G		not specified	Uncertain significance (Apr 07, 2022)
9-92509917-C-T		not specified	Uncertain significance (Jan 10, 2023)
9-92509922-G-A		not specified	Uncertain significance (Aug 14, 2023)
9-92510019-T-A		not specified	Uncertain significance (Nov 30, 2022)
9-92512030-A-G		not specified	Uncertain significance (Jun 07, 2024)
9-92512106-G-T		not specified	Uncertain significance (Jan 20, 2023)
9-92512115-C-T		not specified	Likely benign (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ECM2	protein_coding	protein_coding	ENST00000344604	9	42573

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.33e-9	0.924	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.697	328	365	0.897	0.0000182	4593
Missense in Polyphen		63	88.908	0.70859		1194
Synonymous	0.0211	135	135	0.998	0.00000710	1301
Loss of Function	1.88	18	28.9	0.622	0.00000145	394

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000338	0.000337
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000319	0.000316
Middle Eastern	0.000164	0.000163
South Asian	0.0000662	0.0000653
Other	0.000176	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes matrix assembly and cell adhesiveness. {ECO:0000250}.

Intolerance Scores

• loftool: 0.836
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.26

Haploinsufficiency Scores

• pHI: 0.0875
• hipred: N
• hipred_score: 0.170
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.117

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ecm2

Gene ontology

• Biological process: cell-matrix adhesion;positive regulation of cell-substrate adhesion;extracellular matrix organization
• Cellular component: interstitial matrix;extracellular matrix
• Molecular function: integrin binding;heparin binding;collagen V binding