ECM2

extracellular matrix protein 2

Basic information

Region (hg38): 9:92493554-92536655

Links

ENSG00000106823NCBI:1842OMIM:603479HGNC:3154Uniprot:O94769AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
2
clinvar
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)2478243
9-92500728-G-A not specified Uncertain significance (May 26, 2024)2326747
9-92500760-A-C not specified Uncertain significance (Aug 08, 2022)2305605
9-92500776-G-T not specified Uncertain significance (Apr 23, 2024)2360818
9-92500847-T-C not specified Uncertain significance (Nov 17, 2022)2363413
9-92500859-C-T not specified Uncertain significance (Sep 26, 2023)3086991
9-92500873-A-T not specified Uncertain significance (Jun 24, 2022)2411874
9-92500901-A-C not specified Uncertain significance (May 21, 2024)3274423
9-92500950-G-A not specified Uncertain significance (Feb 23, 2023)2467278
9-92501006-G-A not specified Uncertain significance (Mar 04, 2024)3086990
9-92502558-T-C not specified Uncertain significance (Dec 02, 2022)2401633
9-92502585-A-G not specified Uncertain significance (Aug 15, 2023)2618844
9-92502596-A-T not specified Uncertain significance (Sep 16, 2021)2400340
9-92502615-G-A not specified Uncertain significance (Nov 13, 2023)3086989
9-92505537-A-G not specified Uncertain significance (Jan 23, 2023)2461453
9-92505558-G-A not specified Uncertain significance (Feb 07, 2023)2481767
9-92505585-A-G not specified Uncertain significance (Feb 11, 2022)2277073
9-92505589-G-T not specified Uncertain significance (Jan 30, 2024)3086988
9-92505600-A-G not specified Uncertain significance (Apr 07, 2022)2281663
9-92509917-C-T not specified Uncertain significance (Jan 10, 2023)2463246
9-92509922-G-A not specified Uncertain significance (Aug 14, 2023)2618144
9-92510019-T-A not specified Uncertain significance (Nov 30, 2022)2240526
9-92512030-A-G not specified Uncertain significance (Jun 07, 2024)3274421
9-92512106-G-T not specified Uncertain significance (Jan 20, 2023)2476910
9-92512115-C-T not specified Likely benign (Dec 07, 2021)2212439

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ECM2protein_codingprotein_codingENST00000344604 942573
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.33e-90.9241257000481257480.000191
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6973283650.8970.00001824593
Missense in Polyphen6388.9080.708591194
Synonymous0.02111351350.9980.000007101301
Loss of Function1.881828.90.6220.00000145394

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003380.000337
Ashkenazi Jewish0.000.00
East Asian0.0001640.000163
Finnish0.000.00
European (Non-Finnish)0.0003190.000316
Middle Eastern0.0001640.000163
South Asian0.00006620.0000653
Other0.0001760.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ecm2
Phenotype

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