MMEL1

membrane metalloendopeptidase like 1, the group of M13 metallopeptidases

Basic information

Region (hg38): 1:2590638-2633016

Previous symbols: [ "MMEL2" ]

Links

ENSG00000142606 ∙ NCBI:79258 ∙ OMIM:618104 ∙ HGNC:14668 ∙ Uniprot:Q495T6 ∙ 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 MMEL1 gene.

• Inborn genetic diseases (36 variants)
• not provided (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MMEL1 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				3	6	9
missense			33	4	3	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	33	7	10

Variants in MMEL1

This is a list of pathogenic ClinVar variants found in the MMEL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-2591019-G-A		not specified	Uncertain significance (Aug 16, 2022)
1-2591027-G-T		not specified	Uncertain significance (Mar 11, 2024)
1-2591034-G-A		not specified	Uncertain significance (Sep 17, 2021)
1-2591042-T-C		not specified	Uncertain significance (Aug 17, 2022)
1-2591044-G-T		not specified	Uncertain significance (Dec 17, 2023)
1-2591055-C-T		not specified	Uncertain significance (Aug 30, 2021)
1-2591566-A-G		not specified	Uncertain significance (May 03, 2023)
1-2591579-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-2591603-C-T		not specified	Uncertain significance (Jan 09, 2024)
1-2591624-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-2591922-C-T			Benign (Mar 29, 2018)
1-2591973-C-T			Benign (Mar 29, 2018)
1-2592012-T-C		not specified	Uncertain significance (Jun 12, 2023)
1-2592689-A-G			Likely benign (Feb 25, 2018)
1-2592698-C-G		not specified	Uncertain significance (May 18, 2022)
1-2592725-G-A			Benign (Dec 31, 2019)
1-2592856-A-G		not specified	Uncertain significance (Jul 20, 2021)
1-2592877-A-G		not specified	Likely benign (Nov 22, 2021)
1-2592882-A-G		not specified	Uncertain significance (Jun 24, 2022)
1-2592921-T-G		not specified	Uncertain significance (Sep 01, 2021)
1-2592953-G-T		not specified	Uncertain significance (Jan 24, 2024)
1-2593833-C-T			Benign (Dec 31, 2019)
1-2593847-C-T		not specified	Uncertain significance (Apr 12, 2022)
1-2594421-C-T		not specified	Uncertain significance (Jan 29, 2024)
1-2594426-G-A		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MMEL1	protein_coding	protein_coding	ENST00000378412	23	42404

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.24e-22	0.110	125634	1	113	125748	0.000453

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.126	480	488	0.984	0.0000318	5059
Missense in Polyphen		214	225.91	0.94728		2395
Synonymous	0.0965	203	205	0.991	0.0000144	1470
Loss of Function	1.57	41	53.4	0.768	0.00000300	522

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000656	0.000656
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000381	0.000381
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000542	0.000528
Middle Eastern	0.000381	0.000381
South Asian	0.000621	0.000621
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Metalloprotease involved in sperm function, possibly by modulating the processes of fertilization and early embryonic development. Degrades a broad variety of small peptides with a preference for peptides shorter than 3 kDa containing neutral bulky aliphatic or aromatic amino acid residues. Shares the same substrate specificity with MME and cleaves peptides at the same amide bond (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.200

Intolerance Scores

• loftool: 0.224
• rvis_EVS: -0.66
• rvis_percentile_EVS: 16.09

Haploinsufficiency Scores

• pHI: 0.0834
• hipred: N
• hipred_score: 0.318
• ghis: 0.382

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.137

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mmel1
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular region;integral component of membrane
• Molecular function: metalloendopeptidase activity;metal ion binding