NXPE2

neurexophilin and PC-esterase domain family member 2

Basic information

Region (hg38): 11:114678526-114707069

Previous symbols: [ "FAM55B" ]

Links

ENSG00000204361 ∙ NCBI:120406 ∙ ∙ HGNC:26331 ∙ Uniprot:Q96DL1 ∙ 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 NXPE2 gene.

• Inborn genetic diseases (25 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXPE2 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			24	3		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	4	0

Variants in NXPE2

This is a list of pathogenic ClinVar variants found in the NXPE2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-114679730-A-G		not specified	Likely benign (Aug 13, 2021)
11-114698076-T-G		not specified	Uncertain significance (Jun 06, 2023)
11-114698169-A-G		not specified	Uncertain significance (Jul 12, 2022)
11-114698172-T-G		not specified	Uncertain significance (Mar 16, 2022)
11-114698226-C-T		not specified	Uncertain significance (Dec 01, 2022)
11-114698234-A-G		not specified	Uncertain significance (Sep 25, 2023)
11-114698277-C-T		not specified	Uncertain significance (Oct 27, 2023)
11-114698294-C-A		not specified	Uncertain significance (Feb 14, 2023)
11-114698344-A-T		not specified	Uncertain significance (Aug 12, 2021)
11-114698376-A-G		not specified	Uncertain significance (Jul 19, 2023)
11-114698499-C-G		not specified	Uncertain significance (Jan 22, 2024)
11-114698583-G-A		not specified	Uncertain significance (Jan 23, 2024)
11-114698586-C-A		not specified	Uncertain significance (Oct 29, 2021)
11-114698679-T-G		not specified	Uncertain significance (Jul 25, 2023)
11-114698694-T-C		not specified	Uncertain significance (Mar 07, 2024)
11-114698711-A-T		not specified	Uncertain significance (Feb 15, 2023)
11-114698714-C-T		not specified	Uncertain significance (Mar 24, 2023)
11-114704029-C-G		not specified	Uncertain significance (May 09, 2023)
11-114704031-A-C		not specified	Uncertain significance (May 30, 2023)
11-114704043-C-A		not specified	Uncertain significance (Oct 22, 2021)
11-114705808-A-G		not specified	Uncertain significance (Jul 06, 2021)
11-114705820-A-G		not specified	Uncertain significance (Feb 22, 2023)
11-114705960-C-A		not specified	Uncertain significance (Nov 12, 2021)
11-114705964-A-G		not specified	Uncertain significance (Jun 03, 2022)
11-114706428-T-A		not specified	Uncertain significance (Oct 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXPE2	protein_coding	protein_coding	ENST00000389586	6	30255

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.12e-8	0.335	125595	0	20	125615	0.0000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.162	266	274	0.972	0.0000128	3727
Missense in Polyphen		48	58.995	0.81363		827
Synonymous	0.173	97	99.2	0.978	0.00000490	1019
Loss of Function	0.728	14	17.3	0.811	8.49e-7	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000127	0.000124
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000951	0.0000880
Middle Eastern	0.000167	0.000163
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.44
• rvis_percentile_EVS: 95.06

Haploinsufficiency Scores

• pHI: 0.115
• 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: Nxpe2

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding