NXPE4

neurexophilin and PC-esterase domain family member 4

Basic information

Region (hg38): 11:114570591-114595786

Previous symbols: [ "C11orf33", "FAM55D" ]

Links

ENSG00000137634 ∙ NCBI:54827 ∙ OMIM:618133 ∙ HGNC:23117 ∙ Uniprot:Q6UWF7 ∙ 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 NXPE4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXPE4 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			34	3		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	35	3	0

Variants in NXPE4

This is a list of pathogenic ClinVar variants found in the NXPE4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-114570976-C-T		not specified	Likely benign (Aug 12, 2021)
11-114571001-A-C		not specified	Uncertain significance (Apr 06, 2023)
11-114571041-A-G		not specified	Uncertain significance (Oct 05, 2023)
11-114571089-T-A		not specified	Uncertain significance (Nov 10, 2022)
11-114571117-T-C		not specified	Uncertain significance (Nov 10, 2022)
11-114571170-G-A		not specified	Uncertain significance (Aug 11, 2022)
11-114571171-T-G		not specified	Uncertain significance (Oct 20, 2023)
11-114571194-T-C		not specified	Likely benign (Dec 09, 2024)
11-114571242-A-G		not specified	Uncertain significance (Jul 17, 2024)
11-114571267-C-G		not specified	Uncertain significance (Sep 16, 2021)
11-114571284-A-G		not specified	Uncertain significance (Dec 09, 2023)
11-114571299-C-T		not specified	Uncertain significance (Sep 29, 2023)
11-114571303-C-T		not specified	Uncertain significance (Sep 23, 2023)
11-114571317-G-A		not specified	Likely benign (Feb 03, 2022)
11-114571341-T-G		not specified	Uncertain significance (Jun 06, 2023)
11-114571345-C-G		not specified	Uncertain significance (Jul 19, 2023)
11-114571423-C-T		not specified	Uncertain significance (Sep 02, 2024)
11-114580156-C-T		not specified	Uncertain significance (Jan 26, 2022)
11-114580167-C-T		not specified	Uncertain significance (Dec 28, 2023)
11-114580168-G-A		not specified	Uncertain significance (Dec 17, 2021)
11-114580176-G-C		not specified	Uncertain significance (Jul 25, 2023)
11-114580221-A-G		not specified	Uncertain significance (Oct 21, 2024)
11-114580291-T-C		not specified	Uncertain significance (Sep 20, 2023)
11-114580324-T-C		not specified	Likely benign (Dec 22, 2023)
11-114581736-G-A		not specified	Uncertain significance (Nov 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXPE4	protein_coding	protein_coding	ENST00000375478	5	25172

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.86e-16	0.00420	125652	0	89	125741	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.106	289	284	1.02	0.0000136	3597
Missense in Polyphen		121	105.93	1.1423		1426
Synonymous	-0.489	114	108	1.06	0.00000540	1035
Loss of Function	-0.451	22	19.8	1.11	9.96e-7	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000834	0.000811
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.000386	0.000381
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000276	0.000273
Middle Eastern	0.000386	0.000381
South Asian	0.000799	0.000752
Other	0.000494	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0894

Intolerance Scores

• rvis_EVS: 2.95
• rvis_percentile_EVS: 99.17

Haploinsufficiency Scores

• pHI: 0.0869
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nxpe4

Gene ontology

• Biological process: biological_process
• Cellular component: extracellular exosome
• Molecular function: molecular_function