NXPE1

protein-coding

neurexophilin and PC-esterase domain family member 1

Gene summary

Enables N-acetylneuraminate 9-O-acetyltransferase activity. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

FAM55A

MANE transcript

NM_001395504.1

Inheritance

—

ClinVar variants

U:63B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.31

Max pathogenic AF

—

Genomic locus

chr11:114,518,934-114,559,881

External References & Databases

Ensembl (ENSG00000095110)

Transcript & Mutation Effects

hg38 • Region Span ~40.9 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 NXPE1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 68

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001395504.1. 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					2 clinvar	2
missense			63 clinvar	5 clinvar	1 clinvar	69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	63	5	3	71

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001395504.1	RefSeq	NP_001382433.1	5	MANE Select
ENST00000534921.3	Ensembl	ENSP00000439503.2	5	MANE Select
NM_001367953.1	RefSeq	NP_001354882.1	5	Standard
NM_152315.5	RefSeq	NP_689528.2	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000251921
Coding exons: 4
Length: 38181
Individuals with no LoFs: 125669
Homozygous LoFs: 0
Heterozygous LoFs: 78
Defined: 125747
p: 0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.339	234	220	1.06	0.0000108	2701
Missense (PolyPhen)		71	61.138	1.1613		849
Synonymous	0.303	73	76.4	0.956	0.00000363	755
Loss of Function	-1.01	16	12.2	1.31	5.08e-7	175

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0013	0.0013	notable
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00075	0.00075	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1.09
RVIS percentile EVS: 91.85

Essentials

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

Gene Damage Prediction

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