NANS

N-acetylneuraminate synthase

Basic information

Region (hg38): 9:98056732-98083077

Links

ENSG00000095380

∙ NCBI:54187 ∙ OMIM:605202 ∙ HGNC:19237 ∙ Uniprot:Q9NR45 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

spondyloepimetaphyseal dysplasia, Genevieve type (Moderate), mode of inheritance: AR
spondyloepimetaphyseal dysplasia, Genevieve type (Strong), mode of inheritance: AR
spondyloepimetaphyseal dysplasia, Genevieve type (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spondyloepimetaphyseal dysplasiam Genevieve type	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic	27213289

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NANS gene.

not_provided (140 variants)
Inborn_genetic_diseases (35 variants)
Spondyloepimetaphyseal_dysplasia,_Genevieve_type (20 variants)
NANS-related_disorder (8 variants)
not_specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NANS gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018946.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				37 clinvar	3 clinvar	40
missense	2 clinvar	3 clinvar	78 clinvar	5 clinvar	1 clinvar	89
nonsense	2 clinvar	1 clinvar				3
start loss		1				1
frameshift	3 clinvar	1 clinvar	1 clinvar			5
splice donor/acceptor (+/-2bp)	1 clinvar	1 clinvar				2
Total	8	7	79	42	4

Highest pathogenic variant AF is 0.0000144444

Loading clinvar variants...

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Function: FUNCTION: Produces N-acetylneuraminic acid (Neu5Ac) and 2-keto-3- deoxy-D-glycero-D-galacto-nononic acid (KDN). Can also use N- acetylmannosamine 6-phosphate and mannose 6-phosphate as substrates to generate phosphorylated forms of Neu5Ac and KDN, respectively.;
Pathway: Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Sialuria or French Type Sialuria;Sialuria or French Type Sialuria;Amino Sugar Metabolism;G(M2)-Gangliosidosis: Variant B, Tay-sachs disease;Tay-Sachs Disease;Salla Disease/Infantile Sialic Acid Storage Disease;Aminosugars metabolism;Post-translational protein modification;Metabolism of proteins;CMP-<i>N</i>-acetylneuraminate biosynthesis I (eukaryotes);Sialic acid metabolism;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation (Consensus)

Intolerance Scores

loftool: 0.718
rvis_EVS: 0.42
rvis_percentile_EVS: 77.06

Haploinsufficiency Scores

pHI: 0.189
hipred: N
hipred_score: 0.251
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Nans
Phenotype

Zebrafish Information Network

Gene name: nansa
Affected structure: ceratobranchial cartilage
Phenotype tag: abnormal
Phenotype quality: absent

Gene ontology

Biological process: CMP-N-acetylneuraminate biosynthetic process;carbohydrate biosynthetic process
Cellular component: cytoplasm;cytosol;extracellular exosome
Molecular function: N-acylneuraminate cytidylyltransferase activity;N-acylneuraminate-9-phosphate synthase activity;N-acetylneuraminate synthase activity