NOVA1

protein-coding

NOVA alternative splicing regulator 1

Gene summary

This gene encodes a neuron-specific RNA-binding protein, a member of the Nova family of paraneoplastic disease antigens, that is recognized and inhibited by paraneoplastic antibodies. These antibodies are found in the sera of patients with paraneoplastic opsoclonus-ataxia, breast cancer, and small cell lung cancer. Alternatively spliced transcripts encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002515.3

Inheritance

—

ClinVar variants

U:33B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr14:26,443,090-26,598,033

External References & Databases

Ensembl (ENSG00000139910)

Transcript & Mutation Effects

hg38 • Region Span ~154.9 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 NOVA1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 29

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002515.3. 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						0
missense			30 clinvar	1 clinvar		31
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	33	1	0	34

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002515.3	RefSeq	NP_002506.2	5	MANE Select
ENST00000539517.7	Ensembl	ENSP00000438875.2	5	MANE Select
NM_001366390.2	RefSeq	NP_001353319.1	2	Standard
NM_001366391.2	RefSeq	NP_001353320.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mRNA splicing, via spliceosome
RNA processing
chemical synaptic transmission
locomotory behavior
RNA splicing

Molecular Function

RNA binding
mRNA binding

Cellular Component

nucleus
nucleolus
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000539517
Coding exons: 5
Length: 154662
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125744
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.31	150	254	0.591	0.0000125	3219
Missense (PolyPhen)		15	29.623	0.50637		345
Synonymous	-1.56	115	95.6	1.20	0.00000491	1123
Loss of Function	3.76	0	16.4	0.00	9.37e-7	208

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May regulate RNA splicing or metabolism in a specific subset of developing neurons.;

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.198
RVIS EVS: -0.69
RVIS percentile EVS: 14.97

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.180

Gene Damage Prediction

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