MEP1A

meprin A subunit alpha, the group of Astacins

Basic information

Region (hg38): 6:46793388-46839778

Links

ENSG00000112818 ∙ NCBI:4224 ∙ OMIM:600388 ∙ HGNC:7015 ∙ Uniprot:Q16819 ∙ 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 MEP1A gene.

• Inborn genetic diseases (27 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MEP1A 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				2		2
missense			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	0

Variants in MEP1A

This is a list of pathogenic ClinVar variants found in the MEP1A region.

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

Position	Type	Phenotype	Significance	ClinVar
6-46793466-C-T		not specified	Uncertain significance (Nov 07, 2023)
6-46799116-A-G		not specified	Uncertain significance (Oct 27, 2022)
6-46819651-C-T		not specified	Uncertain significance (Mar 07, 2024)
6-46819657-C-T		not specified	Uncertain significance (Apr 26, 2023)
6-46819663-G-T		not specified	Uncertain significance (Feb 14, 2023)
6-46825284-A-G		not specified	Uncertain significance (Feb 14, 2023)
6-46825296-A-G		not specified	Uncertain significance (Nov 22, 2022)
6-46825298-G-A		not specified	Uncertain significance (Feb 17, 2024)
6-46825326-C-T		not specified	Uncertain significance (Aug 02, 2021)
6-46825401-C-A		not specified	Uncertain significance (Sep 21, 2021)
6-46825407-A-G		not specified	Uncertain significance (Dec 09, 2023)
6-46825433-G-C		not specified	Uncertain significance (Nov 21, 2023)
6-46825455-C-T		not specified	Uncertain significance (Apr 05, 2023)
6-46826366-C-G		not specified	Uncertain significance (Jan 08, 2024)
6-46826437-G-A		not specified	Uncertain significance (May 15, 2023)
6-46826454-C-G		not specified	Uncertain significance (Oct 16, 2023)
6-46826456-G-A		not specified	Uncertain significance (Feb 05, 2024)
6-46826477-A-G		not specified	Uncertain significance (Jun 30, 2022)
6-46829407-C-G		not specified	Uncertain significance (May 26, 2023)
6-46829535-A-G		not specified	Uncertain significance (Dec 14, 2021)
6-46833081-T-C			Likely benign (Apr 16, 2018)
6-46833109-G-C		not specified	Uncertain significance (Aug 10, 2021)
6-46833133-C-T		not specified	Uncertain significance (Aug 02, 2021)
6-46833160-G-A		not specified	Uncertain significance (Mar 29, 2022)
6-46833187-T-A		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MEP1A	protein_coding	protein_coding	ENST00000230588	14	46389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.15e-13	0.879	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.128	406	413	0.982	0.0000221	4944
Missense in Polyphen		143	161.38	0.88612		1983
Synonymous	-1.20	181	162	1.12	0.00000980	1362
Loss of Function	1.96	25	38.0	0.658	0.00000185	432

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000361	0.000361
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000219	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000249	0.000246
Middle Eastern	0.000219	0.000217
South Asian	0.000277	0.000261
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Protein digestion and absorption - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.626
• rvis_EVS: 1.34
• rvis_percentile_EVS: 94.29

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.294

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.565

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mep1a
• Phenotype: immune system phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype; reproductive system phenotype; hematopoietic system phenotype; digestive/alimentary phenotype

Zebrafish Information Network

• Gene name: mep1a.1
• Affected structure: pericardium
• Phenotype tag: abnormal
• Phenotype quality: dilated

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular space;integral component of plasma membrane;meprin A complex;extracellular exosome
• Molecular function: metalloendopeptidase activity;protein binding;zinc ion binding