ECM2

protein-coding

extracellular matrix protein 2

Gene summary

ECM2 encodes extracellular matrix protein 2, so named because it shares extensive similarity with known extracelluar matrix proteins. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2010]

MANE transcript

NM_001393.4

Inheritance

—

ClinVar variants

U:102B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr9:92,493,554-92,536,655

External References & Databases

Ensembl (ENSG00000106823)

Transcript & Mutation Effects

hg38 • Region Span ~43.1 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ECM2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 102

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001393.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			100 clinvar	5 clinvar		105
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	102	5	0	107

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001393.4	RefSeq	NP_001384.1	9	MANE Select
ENST00000344604.10	Ensembl	ENSP00000344758.5	9	MANE Select
NM_001197295.2	RefSeq	NP_001184224.1	9	Standard
NM_001197296.2	RefSeq	NP_001184225.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell-matrix adhesion
positive regulation of cell-substrate adhesion
extracellular matrix organization

Molecular Function

integrin binding
heparin binding
collagen V binding

Cellular Component

interstitial matrix
extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000344604
Coding exons: 9
Length: 42573
Individuals with no LoFs: 125700
Homozygous LoFs: 0
Heterozygous LoFs: 48
Defined: 125748
p: 0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.697	328	365	0.897	0.0000182	4593
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00032	0.00032	rare
South Asian	0.000066	0.000065	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.117

Gene Damage Prediction

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