NBPF10

protein-coding

NBPF member 10, the group of NBPF members

Gene summary

This gene is a member of the neuroblastoma breakpoint family (NBPF) which consists of dozens of recently duplicated genes primarily located in segmental duplications on human chromosome 1. This gene family has experienced its greatest expansion within the human lineage and has expanded, to a lesser extent, among primates in general. Members of this gene family are characterized by tandemly repeated copies of DUF1220 protein domains. Gene copy number variations in the human chromosomal region 1q21.1, where most DUF1220 domains are located, have been implicated in a number of developmental and neurogenetic diseases such as microcephaly, macrocephaly, autism, schizophrenia, cognitive disability, congenital heart disease, neuroblastoma, and congenital kidney and urinary tract anomalies. Altered expression of some gene family members is associated with several types of cancer. This gene family contains numerous pseudogenes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]

MANE transcript

NM_001302371.3

Inheritance

—

ClinVar variants

U:4B:42

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

Max pathogenic AF

—

Genomic locus

chr1:146,064,711-146,229,000

External References & Databases

Ensembl (ENSG00000271425)

NCBI Gene (100132406)

Transcript & Mutation Effects

hg38 • Region Span ~164.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NBPF10 variants in ClinVar

2 Conditions Cataloged

not providedTotal: 46

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001302371.3. Only rare variants are included.

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	25 clinvar		26
missense				14 clinvar	2 clinvar	16
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	4	40	2	46

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001302371.3	RefSeq	NP_001289300.1	90	MANE Select
ENST00000583866.9	Ensembl	ENSP00000463957.6	90	MANE Select
NM_001039703.6	RefSeq	NP_001034792.4	86	Standard
ENST00000612520.2	Ensembl	ENSP00000483006.2	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding

Cellular Component

cytoplasm

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Indispensability pred.: N
Indispensability score: 0.143

Gene Damage Prediction

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