MCEMP1

protein-coding

mast cell expressed membrane protein 1

Gene summary

This gene encodes a single-pass transmembrane protein. Based on its expression pattern, it is speculated to be involved in regulating mast cell differentiation or immune responses. [provided by RefSeq, Jul 2008]

Previous symbols:

C19orf59

MANE transcript

NM_174918.3

Inheritance

—

ClinVar variants

U:15B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr19:7,677,088-7,679,829

External References & Databases

Ensembl (ENSG00000183019)

Transcript & Mutation Effects

hg38 • Region Span ~2.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MCEMP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 16

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174918.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			14 clinvar	2 clinvar		16
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	3	0	18

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174918.3	RefSeq	NP_777578.3	7	MANE Select
ENST00000333598.8	Ensembl	ENSP00000329920.3	7	MANE Select
ENST00000597445.1	Ensembl	ENSP00000471413.1	6	Standard
ENST00000597445.2	Ensembl	ENSP00000471413.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
Innate Immune System
Immune System

Biological Process

neutrophil degranulation

Cellular Component

plasma membrane
integral component of membrane
specific granule membrane
tertiary granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000333598
Coding exons: 7
Length: 3199
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125748
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.285	87	94.8	0.918	0.00000463	1213
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000071	0.000062	rare
Latino/Admixed American	0.000031	0.000029	rare
Ashkenazi Jewish	0.00032	0.00030	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000083	0.000079	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1.08
RVIS percentile EVS: 91.8

Essentials

Essential (gene trap): N