MEPE

matrix extracellular phosphoglycoprotein, the group of SIBLING family

Basic information

Region (hg38): 4:87821397-87846814

Links

ENSG00000152595 ∙ NCBI:56955 ∙ OMIM:605912 ∙ HGNC:13361 ∙ Uniprot:Q9NQ76 ∙ 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 MEPE gene.

• Inborn genetic diseases (30 variants)
• not provided (8 variants)
• MEPE-related condition (3 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MEPE 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			29	4	7	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	5	7

Variants in MEPE

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

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

Position	Type	Phenotype	Significance	ClinVar
4-87838656-A-C		not specified	Uncertain significance (Feb 07, 2023)
4-87844990-A-T		MEPE-related disorder	Benign (Jan 07, 2020)
4-87845004-G-T		not specified	Uncertain significance (Jul 12, 2022)
4-87845045-A-G		MEPE-related disorder	Likely benign (Jan 07, 2020)
4-87845116-G-A		not specified	Uncertain significance (May 09, 2022)
4-87845133-T-C		not specified	Uncertain significance (Aug 12, 2021)
4-87845164-A-T		not specified	Uncertain significance (Feb 10, 2022)
4-87845221-C-T		MEPE-related disorder • not specified	Conflicting classifications of pathogenicity (Sep 27, 2021)
4-87845233-G-A		MEPE-related disorder	Uncertain significance (Nov 01, 2022)
4-87845252-T-C		MEPE-related disorder	Likely benign (Jan 07, 2020)
4-87845298-G-A		MEPE-related disorder	Uncertain significance (Dec 06, 2023)
4-87845347-C-T		not specified	Likely benign (Aug 02, 2021)
4-87845358-C-G		not specified	Uncertain significance (May 22, 2023)
4-87845436-C-T		not specified	Uncertain significance (May 23, 2023)
4-87845448-A-G		not specified	Uncertain significance (Dec 06, 2021)
4-87845484-A-G		MEPE-related disorder	Benign (May 23, 2019)
4-87845485-G-T		not specified	Likely benign (Feb 10, 2022)
4-87845526-A-G		not specified	Uncertain significance (Apr 04, 2023)
4-87845535-C-T		MEPE-related disorder	Likely benign (Aug 12, 2019)
4-87845549-A-C		MEPE-related disorder	Benign (Aug 20, 2019)
4-87845585-C-T		MEPE-related disorder	Likely benign (Jan 07, 2020)
4-87845586-G-T		not specified	Uncertain significance (Jun 06, 2023)
4-87845643-G-A		MEPE-related disorder • not specified	Uncertain significance (Sep 29, 2023)
4-87845680-C-T		not specified	Uncertain significance (Aug 14, 2023)
4-87845719-G-T		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MEPE	protein_coding	protein_coding	ENST00000424957	3	25407

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00863	0.813	125635	0	77	125712	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.188	268	277	0.968	0.0000132	3546
Missense in Polyphen		50	55.167	0.90634		790
Synonymous	0.827	87	97.4	0.893	0.00000488	935
Loss of Function	1.06	4	7.03	0.569	3.82e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000415	0.000413
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000550	0.000545
Middle Eastern	0.00	0.00
South Asian	0.0000992	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes renal phosphate excretion and inhibits intestinal phosphate absorption (PubMed:14962809, PubMed:19005008). Promotes bone mineralization by osteoblasts and cartilage mineralization by chondrocytes (PubMed:18162525, PubMed:19998030, PubMed:22766095). Regulates the mineralization of the extracellular matrix of the craniofacial complex, such as teeth, bone and cartilage (By similarity). Promotes dental pulp stem cell proliferation and differentiation (PubMed:22341070). {ECO:0000250|UniProtKB:Q8K4L6, ECO:0000269|PubMed:14962809, ECO:0000269|PubMed:18162525, ECO:0000269|PubMed:19005008, ECO:0000269|PubMed:19998030, ECO:0000269|PubMed:22341070, ECO:0000269|PubMed:22766095}.
• Pathway: Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.975
• rvis_EVS: 1.67
• rvis_percentile_EVS: 96.29

Haploinsufficiency Scores

• pHI: 0.237
• hipred: N
• hipred_score: 0.169

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00706

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mepe
• Phenotype: hematopoietic system phenotype; skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: skeletal system development;biomineral tissue development;post-translational protein modification;cellular protein metabolic process
• Cellular component: endoplasmic reticulum lumen;extracellular matrix
• Molecular function: extracellular matrix structural constituent;protein binding;extracellular matrix protein binding