NXPE2

protein-coding

neurexophilin and PC-esterase domain family member 2

Gene summary

Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM55B

MANE transcript

NM_182495.6

Inheritance

—

ClinVar variants

U:84B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr11:114,678,527-114,707,069

External References & Databases

Ensembl (ENSG00000204361)

Transcript & Mutation Effects

hg38 • Region Span ~28.5 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 NXPE2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 87

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182495.6. 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			84 clinvar	6 clinvar		90
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	84	7	0	91

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182495.6	RefSeq	NP_872301.2	6	MANE Select
ENST00000389586.6	Ensembl	ENSP00000374237.4	6	MANE Select
ENST00001142169.1	Ensembl	ENSP00000811437.1	6	Standard
XM_011542604.3	RefSeq	XP_011540906.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389586
Coding exons: 6
Length: 30255
Individuals with no LoFs: 125595
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 125615
p: 0.0000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.162	266	274	0.972	0.0000128	3727
Missense (PolyPhen)		48	58.995	0.81363		827
Synonymous	0.173	97	99.2	0.978	0.00000490	1019
Loss of Function	0.728	14	17.3	0.811	8.49e-7	257

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000095	0.000088	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1.44
RVIS percentile EVS: 95.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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