NXPH2

neurexophilin 2

Basic information

Region (hg38): 2:138669156-138780390

Links

ENSG00000144227 ∙ NCBI:11249 ∙ OMIM:604635 ∙ HGNC:8076 ∙ Uniprot:O95156 ∙ 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 NXPH2 gene.

• Inborn genetic diseases (7 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXPH2 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					1	1
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	1

Variants in NXPH2

This is a list of pathogenic ClinVar variants found in the NXPH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-138671010-G-A		not specified	Uncertain significance (May 23, 2023)
2-138671137-T-C		not specified	Uncertain significance (Feb 02, 2022)
2-138671153-G-A			Benign (Oct 19, 2017)
2-138671169-T-C		not specified	Uncertain significance (Jul 30, 2023)
2-138671197-G-T		not specified	Uncertain significance (Sep 26, 2023)
2-138671200-G-C		not specified	Uncertain significance (May 27, 2022)
2-138671257-C-G		not specified	Uncertain significance (Dec 26, 2023)
2-138671286-A-G		not specified	Uncertain significance (Jan 27, 2022)
2-138671493-T-G		not specified	Uncertain significance (Jun 24, 2022)
2-138671521-G-A		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXPH2	protein_coding	protein_coding	ENST00000272641	2	109577

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.926	0.0732	124304	0	1	124305	0.00000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	95	146	0.651	0.00000788	1718
Missense in Polyphen		39	72.348	0.53906		903
Synonymous	0.925	51	60.1	0.848	0.00000350	515
Loss of Function	2.68	0	8.34	0.00	4.36e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000889	0.00000889
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.438
• hipred: Y
• hipred_score: 0.642
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.146

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nxph2

Gene ontology

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