NXPH4

protein-coding

neurexophilin 4

Gene summary

Predicted to enable signaling receptor binding activity. Predicted to be involved in neuropeptide signaling pathway. Predicted to be located in extracellular region. Predicted to be active in GABA-ergic synapse. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_007224.4

Inheritance

—

ClinVar variants

U:40B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr12:57,216,794-57,226,449

External References & Databases

Ensembl (ENSG00000182379)

Transcript & Mutation Effects

hg38 • Region Span ~9.7 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 NXPH4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 38

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007224.4. 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 clinvar		4
missense			37 clinvar	2 clinvar		39
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	40	4	0	44

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007224.4	RefSeq	NP_009155.1	2	MANE Select
ENST00000349394.6	Ensembl	ENSP00000333593.6	2	MANE Select
ENST00000556415.1	Ensembl	ENSP00000452288.1	2	Standard
ENST00001142126.1	Ensembl	ENSP00000807440.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

neuropeptide signaling pathway

Molecular Function

molecular_function
signaling receptor binding

Cellular Component

cellular_component
extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000349394
Coding exons: 2
Length: 9655
Individuals with no LoFs: 125600
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125603
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.46	111	163	0.679	0.00000812	1921
Missense (PolyPhen)		51	83.285	0.61236		978
Synonymous	-0.336	79	75.3	1.05	0.00000390	662
Loss of Function	1.81	2	7.25	0.276	3.10e-7	92

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000055	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000095	0.0000088	rare
South Asian	0.000035	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be signaling molecules that resemble neuropeptides and that act by binding to alpha-neurexins and possibly other receptors. {ECO:0000305}.;

Intolerance Scores

LoFtool: 0.0955
RVIS EVS: -0.1
RVIS percentile EVS: 46.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.222

Gene Damage Prediction

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