NXPE1

neurexophilin and PC-esterase domain family member 1

Basic information

Region (hg38): 11:114518934-114559881

Previous symbols: [ "FAM55A" ]

Links

ENSG00000095110 ∙ NCBI:120400 ∙ ∙ HGNC:28527 ∙ Uniprot:Q8N323 ∙ 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 NXPE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXPE1 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					2	2
missense			27	1	1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	3

Variants in NXPE1

This is a list of pathogenic ClinVar variants found in the NXPE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-114522002-T-C		not specified	Uncertain significance (Jan 31, 2023)
11-114522033-T-C		not specified	Uncertain significance (Apr 18, 2023)
11-114522083-T-C		not specified	Uncertain significance (Jun 06, 2023)
11-114522168-C-G		not specified	Uncertain significance (Feb 13, 2024)
11-114522258-G-A		not specified	Uncertain significance (Mar 25, 2024)
11-114522290-T-C		not specified	Uncertain significance (Dec 03, 2021)
11-114522299-A-G		not specified	Uncertain significance (Aug 20, 2024)
11-114522310-G-C		not specified	Uncertain significance (Jan 23, 2023)
11-114522315-C-T		not specified	Uncertain significance (Jun 11, 2021)
11-114522351-G-A		not specified	Uncertain significance (Feb 11, 2022)
11-114522378-A-G		not specified	Uncertain significance (Apr 09, 2024)
11-114522397-G-A			Benign (May 24, 2018)
11-114522401-G-A		not specified	Uncertain significance (Jan 31, 2024)
11-114522417-T-C		not specified	Uncertain significance (May 21, 2024)
11-114522431-G-A		not specified	Likely benign (Nov 17, 2022)
11-114522460-T-A		not specified	Uncertain significance (Dec 05, 2022)
11-114522489-C-G		not specified	Uncertain significance (May 23, 2024)
11-114522915-G-A		not specified	Uncertain significance (Jun 19, 2024)
11-114522923-G-A		not specified	Uncertain significance (Oct 02, 2023)
11-114522927-C-T		not specified	Uncertain significance (May 26, 2024)
11-114522939-A-G		not specified	Uncertain significance (Apr 11, 2023)
11-114522967-T-C		not specified	Uncertain significance (Feb 21, 2024)
11-114523035-C-T			Benign (Jul 18, 2018)
11-114523088-C-T		not specified	Uncertain significance (Nov 13, 2023)
11-114527869-C-T		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NXPE1	protein_coding	protein_coding	ENST00000251921	4	38181

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.31e-12	0.00703	125669	0	78	125747	0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.339	234	220	1.06	0.0000108	2701
Missense in Polyphen		71	61.138	1.1613		849
Synonymous	0.303	73	76.4	0.956	0.00000363	755
Loss of Function	-1.01	16	12.2	1.31	5.08e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00153	0.00153
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.000163	0.000163
South Asian	0.000755	0.000752
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.09
• rvis_percentile_EVS: 91.85

Haploinsufficiency Scores

• pHI: 0.0627
• 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	High	Medium	High
Cancer	High	High	High

Gene ontology

• Cellular component: extracellular region