NXPH3

neurexophilin 3

Basic information

Region (hg38): 17:49575871-49583827

Links

ENSG00000182575 ∙ NCBI:11248 ∙ OMIM:604636 ∙ HGNC:8077 ∙ Uniprot:O95157 ∙ 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 NXPH3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXPH3 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						0
missense			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in NXPH3

This is a list of pathogenic ClinVar variants found in the NXPH3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-49578603-G-A		not specified	Uncertain significance (May 26, 2022)
17-49578626-G-A		not specified	Uncertain significance (Dec 16, 2024)
17-49578630-C-T		not specified	Uncertain significance (Feb 21, 2024)
17-49578635-G-A		not specified	Uncertain significance (Dec 20, 2021)
17-49578656-G-A		not specified	Likely benign (Apr 07, 2023)
17-49578669-G-A		not specified	Uncertain significance (Feb 12, 2024)
17-49578675-G-A		not specified	Uncertain significance (Oct 25, 2022)
17-49578753-C-T		not specified	Uncertain significance (Mar 26, 2024)
17-49578773-A-G		not specified	Likely benign (Dec 16, 2023)
17-49578779-G-A		not specified	Uncertain significance (Dec 14, 2023)
17-49578785-C-T		not specified	Uncertain significance (Jul 09, 2021)
17-49578795-G-A		not specified	Uncertain significance (Feb 03, 2022)
17-49578807-G-A		not specified	Uncertain significance (Jul 15, 2021)
17-49578851-G-A		not specified	Uncertain significance (Jun 06, 2023)
17-49578878-G-A		not specified	Uncertain significance (Aug 12, 2021)
17-49578909-T-C		not specified	Uncertain significance (Oct 17, 2023)
17-49578912-A-G		not specified	Uncertain significance (Aug 08, 2023)
17-49578935-G-A		not specified	Uncertain significance (Feb 05, 2024)
17-49579094-G-A		not specified	Uncertain significance (Jun 21, 2022)
17-49579133-A-G		not specified	Uncertain significance (Jun 13, 2022)
17-49579181-C-A		not specified	Uncertain significance (Aug 01, 2024)
17-49579196-G-A		not specified	Uncertain significance (Apr 08, 2022)
17-49579263-A-G		not specified	Uncertain significance (Feb 15, 2023)
17-49579278-C-G		not specified	Uncertain significance (Nov 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXPH3	protein_coding	protein_coding	ENST00000328741	2	7970

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.284	0.696	125730	0	3	125733	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.563	140	160	0.875	0.0000105	1632
Missense in Polyphen		46	61.724	0.74525		687
Synonymous	2.11	44	65.8	0.669	0.00000424	513
Loss of Function	1.96	2	7.98	0.251	4.28e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be signaling molecules that resemble neuropeptides. Ligand for alpha-neurexins (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.0581
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.429
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nxph3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype

Gene ontology

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