NXPH1

neurexophilin 1

Basic information

Region (hg38): 7:8433609-8752961

Links

ENSG00000122584 ∙ NCBI:30010 ∙ OMIM:604639 ∙ HGNC:20693 ∙ Uniprot:P58417 ∙ 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 NXPH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXPH1 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	2	3
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	2

Variants in NXPH1

This is a list of pathogenic ClinVar variants found in the NXPH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-8435727-G-A		not specified	Uncertain significance (Jun 09, 2022)
7-8435763-A-G		not specified	Uncertain significance (Dec 04, 2024)
7-8751014-T-A		not specified	Uncertain significance (Dec 04, 2024)
7-8751035-G-A		not specified	Uncertain significance (Jan 26, 2023)
7-8751044-G-A		not specified	Uncertain significance (Jan 02, 2024)
7-8751059-G-A		not specified	Uncertain significance (May 06, 2024)
7-8751067-C-A		not specified	Uncertain significance (Dec 08, 2023)
7-8751110-T-G		not specified	Uncertain significance (Feb 02, 2024)
7-8751184-C-A		not specified	Uncertain significance (Sep 26, 2024)
7-8751232-C-G		not specified	Uncertain significance (Nov 16, 2021)
7-8751289-G-A			Likely benign (Jan 03, 2019)
7-8751352-G-A			Benign (Dec 31, 2019)
7-8751356-C-G		not specified	Uncertain significance (Aug 21, 2024)
7-8751395-A-G		not specified	Uncertain significance (Aug 17, 2021)
7-8751499-C-T			Benign (Dec 31, 2019)
7-8751500-G-A		not specified	Uncertain significance (Mar 20, 2024)
7-8751507-A-G		not specified	Uncertain significance (Nov 25, 2024)
7-8751537-G-A		not specified	Uncertain significance (Aug 10, 2021)
7-8751744-A-G		not specified	Uncertain significance (Mar 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXPH1	protein_coding	protein_coding	ENST00000405863	2	319009

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.484	0.512	124575	0	2	124577	0.00000803

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.267	134	143	0.937	0.00000720	1782
Missense in Polyphen		44	60.265	0.7301		791
Synonymous	-0.909	66	57.3	1.15	0.00000308	510
Loss of Function	2.38	2	10.2	0.196	5.18e-7	125

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)	0.0000178	0.0000177
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}.

Intolerance Scores

• loftool: 0.133
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.436
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.766

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nxph1
• Phenotype: reproductive system phenotype

Gene ontology

• Cellular component: extracellular region
• Molecular function: signaling receptor binding