NXPE3

neurexophilin and PC-esterase domain family member 3

Basic information

Region (hg38): 3:101779177-101843743

Previous symbols: [ "FAM55C" ]

Links

ENSG00000144815 ∙ NCBI:91775 ∙ ∙ HGNC:28238 ∙ Uniprot:Q969Y0 ∙ 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 NXPE3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXPE3 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			24	1		25
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	1	0

Variants in NXPE3

This is a list of pathogenic ClinVar variants found in the NXPE3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-101785673-A-G		not specified	Uncertain significance (Nov 09, 2021)
3-101801299-A-G		not specified	Uncertain significance (Dec 14, 2023)
3-101801314-G-A		not specified	Uncertain significance (Dec 20, 2023)
3-101801352-T-C		not specified	Uncertain significance (Jul 17, 2023)
3-101801364-C-T		not specified	Uncertain significance (May 23, 2023)
3-101801448-C-G		not specified	Uncertain significance (Oct 12, 2021)
3-101801489-C-A		not specified	Uncertain significance (May 24, 2023)
3-101801547-C-A		not specified	Uncertain significance (Mar 26, 2024)
3-101801547-C-G		not specified	Uncertain significance (May 23, 2023)
3-101801577-G-C		not specified	Uncertain significance (Mar 20, 2023)
3-101801592-CTCAAGCTG-C		Abnormality of neuronal migration	Benign (Oct 31, 2014)
3-101801602-AG-A		Abnormality of neuronal migration	Benign (Oct 31, 2014)
3-101801635-A-G		not specified	Uncertain significance (Nov 02, 2023)
3-101801745-G-C		not specified	Uncertain significance (Mar 29, 2024)
3-101801760-A-G		not specified	Uncertain significance (Mar 29, 2022)
3-101801763-G-A		not specified	Uncertain significance (Jun 24, 2022)
3-101801898-A-C		not specified	Uncertain significance (Mar 27, 2023)
3-101801898-A-G		not specified	Uncertain significance (Oct 29, 2021)
3-101801908-C-G		not specified	Uncertain significance (May 21, 2024)
3-101801920-G-C		not specified	Uncertain significance (Feb 23, 2023)
3-101801933-C-G		not specified	Uncertain significance (Jun 27, 2022)
3-101816828-G-C		Abnormality of neuronal migration	Benign (Oct 31, 2014)
3-101821473-A-G		not specified	Uncertain significance (Jun 09, 2022)
3-101821491-G-T		not specified	Uncertain significance (Mar 16, 2022)
3-101821511-C-T		not specified	Uncertain significance (Nov 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXPE3	protein_coding	protein_coding	ENST00000422132	5	49028

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0134	0.985	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.441	288	310	0.929	0.0000174	3675
Missense in Polyphen		95	114.73	0.82805		1358
Synonymous	-0.270	122	118	1.03	0.00000627	1125
Loss of Function	2.82	7	20.9	0.334	0.00000112	243

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.55

Haploinsufficiency Scores

• pHI: 0.0901
• hipred: Y
• hipred_score: 0.595
• ghis: 0.553

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: Nxpe3

Gene ontology

• Cellular component: extracellular region