ERMP1

endoplasmic reticulum metallopeptidase 1, the group of M28 metallopeptidases

Basic information

Region (hg38): 9:5749832-5879537

Previous symbols: [ "KIAA1815" ]

Links

ENSG00000099219 ∙ NCBI:79956 ∙ OMIM:611156 ∙ HGNC:23703 ∙ Uniprot:Q7Z2K6 ∙ 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 ERMP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERMP1 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	3	5
missense			41	1	2	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding		1	53	11	3	68
Total	0	1	94	14	8

Variants in ERMP1

This is a list of pathogenic ClinVar variants found in the ERMP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-5753220-G-C		not specified	Uncertain significance (Jan 27, 2022)
9-5753555-T-C		not specified	Uncertain significance (Jul 09, 2021)
9-5753593-G-A		not specified	Uncertain significance (Dec 20, 2023)
9-5754894-C-A			Benign (Oct 17, 2017)
9-5756257-C-T		not specified	Uncertain significance (Feb 27, 2024)
9-5756324-G-C		not specified	Uncertain significance (Jan 03, 2024)
9-5756327-C-G		RIC1-related disorder	Likely benign (Mar 21, 2022)
9-5756369-A-G		not specified	Uncertain significance (Oct 21, 2021)
9-5757337-A-G			Likely benign (Aug 01, 2024)
9-5757362-C-T		not specified	Uncertain significance (Dec 21, 2022)
9-5757363-G-A		not specified	Uncertain significance (Jul 01, 2023)
9-5757386-G-A		not specified	Uncertain significance (Dec 27, 2023)
9-5757391-A-G			Likely benign (Jan 01, 2024)
9-5757428-A-G		not specified	Uncertain significance (Jan 05, 2022)
9-5762533-A-C		Catifa syndrome	Benign (Aug 19, 2021)
9-5762595-C-T		Seizure	Uncertain significance (-)
9-5762616-C-A		not specified	Uncertain significance (Mar 02, 2023)
9-5762621-C-G		not specified	Uncertain significance (Feb 03, 2022)
9-5762623-G-A		not specified	Uncertain significance (Feb 10, 2023)
9-5763299-C-T		not specified	Uncertain significance (Dec 16, 2022)
9-5763304-G-T		not specified	Uncertain significance (May 20, 2024)
9-5763331-C-T			Likely benign (May 01, 2023)
9-5763360-C-T		Catifa syndrome	Likely pathogenic (Jun 08, 2022)
9-5763368-G-C		not specified	Uncertain significance (Jan 04, 2024)
9-5763451-A-C		not specified	Uncertain significance (Sep 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERMP1	protein_coding	protein_coding	ENST00000339450	15	68042

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.63e-12	0.938	125623	0	125	125748	0.000497

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.842	519	468	1.11	0.0000227	5846
Missense in Polyphen		65	90.414	0.71892		1150
Synonymous	-2.59	217	174	1.25	0.00000873	1808
Loss of Function	2.12	25	39.4	0.635	0.00000198	477

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00153	0.00153
Ashkenazi Jewish	0.00	0.00
East Asian	0.000344	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000665	0.000659
Middle Eastern	0.000344	0.000326
South Asian	0.000296	0.000294
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Within the ovary, required for the organization of somatic cells and oocytes into discrete follicular structures. {ECO:0000250|UniProtKB:Q6UPR8}.

Recessive Scores

• pRec: 0.0949

Intolerance Scores

• loftool: 0.869
• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.8

Haploinsufficiency Scores

• pHI: 0.172
• hipred: N
• hipred_score: 0.492
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.182

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ermp1
• Phenotype: craniofacial phenotype; growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; vision/eye phenotype; renal/urinary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: proteolysis
• Cellular component: endoplasmic reticulum membrane;membrane;integral component of membrane
• Molecular function: metallopeptidase activity;metal ion binding