NXPE4

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			73 clinvar	6 clinvar		79
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	74	6	0	80

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001077639.2	RefSeq	NP_001071107.1	5	MANE Select
ENST00000375478.4	Ensembl	ENSP00000364627.3	5	MANE Select
NM_017678.3	RefSeq	NP_060148.2	3	Standard
ENST00000424261.6	Ensembl	ENSP00000401503.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375478
Coding exons: 5
Length: 25172
Individuals with no LoFs: 125652
Homozygous LoFs: 0
Heterozygous LoFs: 89
Defined: 125741
p: 0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.106	289	284	1.02	0.0000136	3597
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00052	0.00049	rare
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.00039	0.00038	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00028	0.00027	rare
South Asian	0.00080	0.00075	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0894

Intolerance Scores

RVIS EVS: 2.95
RVIS percentile EVS: 99.17

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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