MCEMP1

mast cell expressed membrane protein 1

Basic information

Region (hg38): 19:7677088-7679829

Previous symbols: [ "C19orf59" ]

Links

ENSG00000183019 ∙ NCBI:199675 ∙ OMIM:609565 ∙ HGNC:27291 ∙ Uniprot:Q8IX19 ∙ 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 MCEMP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCEMP1 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			7	2		9
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	1

Variants in MCEMP1

This is a list of pathogenic ClinVar variants found in the MCEMP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-7677148-A-C		not specified	Uncertain significance (Jan 20, 2023)
19-7677166-A-C		not specified	Uncertain significance (Nov 18, 2022)
19-7678117-C-G		not specified	Uncertain significance (Feb 26, 2024)
19-7678160-A-G		not specified	Uncertain significance (Jan 20, 2023)
19-7678235-G-A		not specified	Likely benign (Jan 09, 2024)
19-7678376-G-A		not specified	Uncertain significance (Mar 17, 2023)
19-7678553-A-G		not specified	Uncertain significance (Nov 03, 2022)
19-7678565-G-C		not specified	Uncertain significance (Jul 29, 2023)
19-7678593-C-T			Likely benign (Jul 01, 2022)
19-7678983-C-T			Benign (Mar 28, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MCEMP1	protein_coding	protein_coding	ENST00000333598	7	3199

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000142	0.871	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.285	87	94.8	0.918	0.00000463	1213
Missense in Polyphen		18	18.302	0.98352		250
Synonymous	-1.09	46	37.5	1.23	0.00000200	329
Loss of Function	1.39	8	13.5	0.592	7.17e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000103	0.0000926
Ashkenazi Jewish	0.000315	0.000298
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000834	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Intolerance Scores

• rvis_EVS: 1.08
• rvis_percentile_EVS: 91.8

Haploinsufficiency Scores

• pHI: 0.0164
• hipred: N
• hipred_score: 0.145

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Mcemp1

Gene ontology

• Biological process: neutrophil degranulation
• Cellular component: plasma membrane;integral component of membrane;specific granule membrane;tertiary granule membrane