NEU3

protein-coding

neuraminidase 3, the group of Neuraminidases

Gene summary

This gene product belongs to a family of glycohydrolytic enzymes which remove sialic acid residues from glycoproteins and glycolipids. It is localized in the plasma membrane, and its activity is specific for gangliosides. It may play a role in modulating the ganglioside content of the lipid bilayer. [provided by RefSeq, Jul 2008]

MANE transcript

NM_006656.6

Inheritance

—

ClinVar variants

U:84B:6

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.85

Max pathogenic AF

—

Genomic locus

chr11:74,988,279-75,018,893

External References & Databases

Ensembl (ENSG00000162139)

Transcript & Mutation Effects

hg38 • Region Span ~30.6 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 NEU3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 86

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

Marfanoid habitus and intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006656.6. 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			84 clinvar	6 clinvar		90
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	84	6	0	90

Loading ClinVar variants...

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_006656.6	RefSeq	NP_006647.3	3	MANE Select
ENST00000294064.9	Ensembl	ENSP00000294064.4	3	MANE Select
NM_001367860.1	RefSeq	NP_001354789.1	3	Standard
NM_001367861.1	RefSeq	NP_001354790.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Other glycan degradation - Homo sapiens (human)
Sphingolipid metabolism - Homo sapiens (human)
Sphingolipid Metabolism
Gaucher Disease
Globoid Cell Leukodystrophy

Biological Process

carbohydrate metabolic process
glycosphingolipid metabolic process
ganglioside catabolic process
oligosaccharide catabolic process

Molecular Function

exo-alpha-sialidase activity
alpha-sialidase activity
exo-alpha-(2->3)-sialidase activity
exo-alpha-(2->6)-sialidase activity
exo-alpha-(2->8)-sialidase activity

Cellular Component

cytoplasm
plasma membrane
membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000294064
Coding exons: 3
Length: 30760
Individuals with no LoFs: 124564
Homozygous LoFs: 1
Heterozygous LoFs: 131
Defined: 124696
p: 0.000529

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0967	256	260	0.983	0.0000139	2996
Missense (PolyPhen)		97	101.33	0.95729		1153
Synonymous	-0.152	105	103	1.02	0.00000497	955
Loss of Function	0.562	13	15.4	0.845	8.09e-7	174

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00019	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00083	0.00083	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.0028	0.0028	notable
Other	0.00050	0.00050	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in modulating the ganglioside content of the lipid bilayer at the level of membrane-bound sialyl glycoconjugates. {ECO:0000269|PubMed:10861246, ECO:0000269|PubMed:20511247}.;

Recessive Scores

pRec: 0.304

Intolerance Scores

LoFtool: 0.373
RVIS EVS: -0.13
RVIS percentile EVS: 43.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.655

Gene Damage Prediction

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