NXPH4

neurexophilin 4

Basic information

Region (hg38): 12:57216794-57226449

Links

ENSG00000182379 ∙ NCBI:11247 ∙ OMIM:604637 ∙ HGNC:8078 ∙ Uniprot:O95158 ∙ 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 NXPH4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXPH4 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				2		2
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in NXPH4

This is a list of pathogenic ClinVar variants found in the NXPH4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57224954-C-T		not specified	Uncertain significance (Oct 22, 2021)
12-57224956-C-G		not specified	Uncertain significance (Jun 11, 2024)
12-57225067-G-A		not specified	Uncertain significance (Dec 17, 2023)
12-57225068-C-A		not specified	Uncertain significance (Dec 17, 2023)
12-57225118-G-A		not specified	Uncertain significance (Feb 27, 2023)
12-57225324-G-C			Likely benign (May 01, 2022)
12-57225328-G-C		not specified	Uncertain significance (Aug 26, 2022)
12-57225361-G-C		not specified	Uncertain significance (Aug 12, 2021)
12-57225391-C-A		not specified	Uncertain significance (Sep 06, 2022)
12-57225416-C-A		not specified	Uncertain significance (Sep 26, 2023)
12-57225451-G-T		not specified	Uncertain significance (Feb 16, 2023)
12-57225502-T-G		not specified	Uncertain significance (Oct 05, 2021)
12-57225503-C-T		not specified	Uncertain significance (Aug 23, 2021)
12-57225506-G-A		not specified	Uncertain significance (Jul 06, 2021)
12-57225642-C-A		not specified	Uncertain significance (Jun 17, 2024)
12-57225663-C-G			Likely benign (Oct 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXPH4	protein_coding	protein_coding	ENST00000349394	2	9655

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.230	0.739	125600	0	3	125603	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	111	163	0.679	0.00000812	1921
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.00000953	0.00000880
Middle Eastern	0.0000549	0.0000545
South Asian	0.0000346	0.0000327
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0667
• hipred: N
• hipred_score: 0.464
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.222

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nxph4
• Phenotype: homeostasis/metabolism phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: neuropeptide signaling pathway
• Cellular component: cellular_component;extracellular region
• Molecular function: molecular_function;signaling receptor binding