NPL

gene
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Also known as NPL1DHDPS1

Summary

NPL (N-acetylneuraminate pyruvate lyase, HGNC:16781) is a protein-coding gene on chromosome 1q25.3, encoding N-acetylneuraminate lyase (Q9BXD5). Catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetylmannosamine via a Schiff base intermediate.

This gene encodes a member of the N-acetylneuraminate lyase sub-family of (beta/alpha)(8)-barrel enzymes. N-acetylneuraminate lyases regulate cellular concentrations of N-acetyl-neuraminic acid (sialic acid) by mediating the reversible conversion of sialic acid into N-acetylmannosamine and pyruvate. A pseudogene of this gene is located on the short arm of chromosome 2. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 80896 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 58 total
  • MANE Select transcript: NM_030769

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16781
Approved symbolNPL
NameN-acetylneuraminate pyruvate lyase
Location1q25.3
Locus typegene with protein product
StatusApproved
AliasesNPL1, DHDPS1
Ensembl geneENSG00000135838
Ensembl biotypeprotein_coding
OMIM611412
Entrez80896

Gene structure

Transcript identifiers

Ensembl transcripts: 45 — 39 protein_coding, 6 protein_coding_CDS_not_defined

ENST00000258317, ENST00000367552, ENST00000367553, ENST00000367554, ENST00000367555, ENST00000460179, ENST00000460690, ENST00000463899, ENST00000471010, ENST00000479721, ENST00000488424, ENST00000614468, ENST00000879498, ENST00000879499, ENST00000879500, ENST00000879501, ENST00000879502, ENST00000879503, ENST00000879504, ENST00000879505, ENST00000879506, ENST00000879507, ENST00000879508, ENST00000879509, ENST00000879510, ENST00000879511, ENST00000879512, ENST00000879513, ENST00000879514, ENST00000879515, ENST00000879516, ENST00000879517, ENST00000879518, ENST00000879519, ENST00000913310, ENST00000949073, ENST00000949074, ENST00000949075, ENST00000949076, ENST00000949077, ENST00000949078, ENST00000949079, ENST00000949080, ENST00000949081, ENST00000949082

RefSeq mRNA: 5 — MANE Select: NM_030769 NM_001200050, NM_001200051, NM_001200052, NM_001200056, NM_030769

CCDS: CCDS1350, CCDS55666, CCDS55667, CCDS72990

Canonical transcript exons

ENST00000367553 — 13 exons

ExonStartEnd
ENSE00001445014182792232182792286
ENSE00001926869182789773182789805
ENSE00002297266182828724182830384
ENSE00003460025182825781182825820
ENSE00003466245182816714182816806
ENSE00003535241182803698182803771
ENSE00003554575182806145182806232
ENSE00003567390182818541182818689
ENSE00003570256182812156182812213
ENSE00003615333182818813182818859
ENSE00003630071182814783182814858
ENSE00003634847182794356182794439
ENSE00003665852182822115182822199

Expression profiles

Bgee: expression breadth ubiquitous, 244 present calls, max score 97.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.1140 / max 1758.7315, expressed in 1262 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
704529.11401262

Top tissues by expression

277 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
monocyteCL:000057697.87gold quality
mononuclear cellCL:000084297.26gold quality
leukocyteCL:000073896.95gold quality
bloodUBERON:000017895.73gold quality
granulocyteCL:000009491.67gold quality
spleenUBERON:000210691.60gold quality
spermCL:000001989.82silver quality
gall bladderUBERON:000211088.70gold quality
right lungUBERON:000216788.52gold quality
C1 segment of cervical spinal cordUBERON:000646988.26gold quality
adult mammalian kidneyUBERON:000008288.13gold quality
secondary oocyteCL:000065588.08gold quality
lymph nodeUBERON:000002987.89gold quality
gingival epitheliumUBERON:000194987.82silver quality
nephron tubuleUBERON:000123187.38gold quality
lateral nuclear group of thalamusUBERON:000273687.18gold quality
bone marrowUBERON:000237187.15gold quality
trabecular bone tissueUBERON:000248387.10gold quality
caudate nucleusUBERON:000187387.04gold quality
upper leg skinUBERON:000426286.88gold quality
superficial temporal arteryUBERON:000161486.86gold quality
upper lobe of left lungUBERON:000895286.77gold quality
placentaUBERON:000198786.76gold quality
upper lobe of lungUBERON:000894886.75gold quality
male germ cellCL:000001586.40silver quality
spinal cordUBERON:000224086.22gold quality
visceral pleuraUBERON:000240186.05gold quality
gingivaUBERON:000182885.91silver quality
parietal pleuraUBERON:000240085.53gold quality
lower lobe of lungUBERON:000894985.41gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 6.

ExperimentMarker?Max mean expression
E-MTAB-6701yes55.08
E-MTAB-6678yes39.45
E-HCAD-25yes24.66
E-CURD-112yes14.95
E-MTAB-9388yes7.76
E-HCAD-10no2.12
E-MTAB-9467no0.91
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

87 targeting NPL, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3646100.0073.565283
HSA-MIR-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-366299.9973.825684
HSA-MIR-477599.9875.006394
HSA-MIR-548AN99.9770.912817
HSA-MIR-60799.9773.625593
HSA-MIR-590-3P99.9674.346478
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-570-3P99.9672.414910
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-539-5P99.9370.302855
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-808799.9069.551351
HSA-MIR-427199.8868.322244
HSA-MIR-579-3P99.8671.663628
HSA-MIR-659-3P99.8570.691620
HSA-MIR-664B-3P99.8471.653590

Literature-anchored findings (GeneRIF, showing 2)

  • an NPL splice variant is mainly expressed in human liver, kidney and peripheral blood leukocytes (PMID:16147865)
  • 3D structure model of N-acetylneuraminate lyase from human (hNAL, EC 4.1.3.3) was created and refined (PMID:19057931)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerionplENSDARG00000009390
mus_musculusNplENSMUSG00000042684
rattus_norvegicusNplENSRNOG00000002775

Paralogs (1): HOGA1 (ENSG00000241935)

Protein

Protein identifiers

N-acetylneuraminate lyaseQ9BXD5 (reviewed: Q9BXD5)

Alternative names: N-acetylneuraminate pyruvate-lyase, N-acetylneuraminic acid aldolase, Sialate lyase, Sialate-pyruvate lyase, Sialic acid aldolase, Sialic acid lyase

All UniProt accessions (2): A0A087WZ70, Q9BXD5

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetylmannosamine via a Schiff base intermediate. It prevents sialic acids from being recycled and returning to the cell surface. Involved in the N-glycolylneuraminic acid (Neu5Gc) degradation pathway. Although human is not able to catalyze formation of Neu5Gc due to the inactive CMAHP enzyme, Neu5Gc is present in food and must be degraded.

Subunit / interactions. Homotetramer.

Subcellular location. Cytoplasm.

Tissue specificity. Isoform 2 is expressed in placenta, liver, kidney, pancreas, spleen, thymus, ovary, small intestine and peripheral blood leukocyte.

Pathway. Amino-sugar metabolism; N-acetylneuraminate degradation.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the DapA family. NanA subfamily.

Isoforms (5)

UniProt IDNamesCanonical?
Q9BXD5-11yes
Q9BXD5-22
Q9BXD5-33
Q9BXD5-44
Q9BXD5-55

RefSeq proteins (5): NP_001186979, NP_001186980, NP_001186981, NP_001186985, NP_110396* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002220DapA-likeFamily
IPR005264NanAFamily
IPR013785Aldolase_TIMHomologous_superfamily

Pfam: PF00701

Enzyme classification (BRENDA):

  • EC 4.1.3.3 — N-acetylneuraminate lyase (BRENDA: 30 organisms, 144 substrates, 77 inhibitors, 161 Km, 114 kcat entries)

Substrate kinetics (BRENDA)

21 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
N-ACETYLNEURAMINIC ACID0.4–110034
N-ACETYLNEURAMINATE0.013–87.730
N-ACETYL-D-MANNOSAMINE6.9–320015
N-ACETYL-D-NEURAMINIC ACID2.1–59.514
PYRUVATE0.5–72.413
(5R,6R)-7-(DIPROPYLAMINO)-4,5,6-TRIHYDROXY-2,7-D0.2–1110
(2S,4S,5R,6R)-5-(ACETYLAMINO)-6-[(DIPROPYLAMINO)0.35–10.66
D-3-DEOXY-MANNO-2-OCTULOSONIC ACID3.5–14.56
L-3-DEOXY-MANNO-2-OCTULOSONIC ACID2.4–14.16
N-ACETYL-L-NEURAMINIC ACID4.4–369.44
N-GLYCOLYLNEURAMINIC ACID2.2–4.64
(2R,3R,4R)-6-[(AMINOOXY)CARBONYL]-3,4,6-TRIHYDRO0.39–112
SIALIC ACID4.4–382
N-ACETYL-4-O-ACETYLNEURAMINIC ACID12.51
N-ACETYL-7-O-ACETYLNEURAMINIC ACID4.51

Catalyzed reactions (Rhea), 1 shown:

  • aceneuramate = aldehydo-N-acetyl-D-mannosamine + pyruvate (RHEA:23296)

UniProt features (46 total): helix 16, strand 9, binding site 7, splice variant 5, sequence conflict 4, active site 2, turn 2, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
6ARHX-RAY DIFFRACTION1.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BXD5-F193.610.90

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 143 (proton donor); 173 (schiff-base intermediate with substrate)

Ligand- & substrate-binding residues (7): 51; 52; 175; 199; 201; 202; 218

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-4085001Sialic acid metabolism

MSigDB gene sets: 224 (showing top): MODULE_418, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, ADDYA_ERYTHROID_DIFFERENTIATION_BY_HEMIN, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP, GOBP_AMIDE_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_CATABOLIC_PROCESS, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, GOBP_AMINO_SUGAR_CATABOLIC_PROCESS, GOBP_AMINO_SUGAR_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GATA1_03, GOBP_SMALL_MOLECULE_CATABOLIC_PROCESS, DODD_NASOPHARYNGEAL_CARCINOMA_UP, BROWN_MYELOID_CELL_DEVELOPMENT_DN

GO Biological Process (2): carbohydrate metabolic process (GO:0005975), N-acetylneuraminate catabolic process (GO:0019262)

GO Molecular Function (4): N-acetylneuraminate lyase activity (GO:0008747), identical protein binding (GO:0042802), protein binding (GO:0005515), lyase activity (GO:0016829)

GO Cellular Component (2): cytosol (GO:0005829), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Synthesis of substrates in N-glycan biosythesis1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
primary metabolic process1
N-acetylneuraminate metabolic process1
amino sugar catabolic process1
carboxylic acid catabolic process1
oxo-acid-lyase activity1
protein binding1
binding1
catalytic activity1
cytoplasm1
intracellular anatomical structure1

Protein interactions and networks

STRING

1362 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NPLCMASQ8NFW8524
NPLACRP10323480
NPLGNEQ9Y223465
NPLNANPQ8TBE9456
NPLNANSQ9NR45445
NPLST8SIA5O15466445
NPLZBTB8BQ8NAP8418
NPLPRAP1Q96NZ9405
NPLSLC35A1P78382399
NPLSLC17A5Q9NRA2372
NPLNEU1Q99519362
NPLRENBPP51606356
NPLMBOAT1Q6ZNC8355
NPLPOLNQ7Z5Q5355
NPLPRKRIP1Q9H875355

IntAct

11 interactions, top by confidence:

ABTypeScore
NPLNPLpsi-mi:“MI:0915”(physical association)0.670
NPLNTAQ1psi-mi:“MI:0915”(physical association)0.560
NTAQ1NPLpsi-mi:“MI:0915”(physical association)0.560
NPLPEG10psi-mi:“MI:0915”(physical association)0.400
NPLCFAP418psi-mi:“MI:0915”(physical association)0.370
NPLODR4psi-mi:“MI:0914”(association)0.350
NPLNPLpsi-mi:“MI:0915”(physical association)0.000

BioGRID (13): NPL (Two-hybrid), NPL (Two-hybrid), PEG10 (Affinity Capture-MS), QPRT (Affinity Capture-MS), NPL (Proximity Label-MS), NPL (Two-hybrid), PEG10 (Affinity Capture-MS), UFSP2 (Affinity Capture-MS), C1orf27 (Affinity Capture-MS), NPL (Proximity Label-MS), NPL (Proximity Label-MS), NPL (Proximity Label-MS), APP (Reconstituted Complex)

ESM2 similar proteins: A4IT57, A8NEP3, B0B8N1, B0BAB0, B0BBG3, B0SBH6, B0SJ25, B3EK39, B4GP48, B4S3A5, G5EDZ2, O13831, O34873, P00480, P0CD74, P16578, P54724, Q11185, Q1RMS2, Q254V9, Q25566, Q29BL3, Q29RY9, Q3B8E8, Q3KL39, Q5F3Z1, Q5L789, Q5M8W9, Q5M905, Q5RDY1, Q5XGL6, Q5XGL8, Q5ZKD4, Q66H59, Q6MD01, Q6MEB3, Q6NY77, Q6NYR8, Q7SZS2, Q822T2

Diamond homologs: A1AGB9, A1ATI8, A3N352, A4WF38, A5GD89, A5IPI2, A6QDU7, A6TY99, A7B555, A7WXZ2, A7Z4U8, A7ZSB8, A8A535, A8AQB6, A8YZD9, A9MNY6, A9N833, B0BSI2, B0R3D6, B0UTI7, B1IQQ4, B1LGJ0, B1XHJ8, B2U1V9, B3E936, B3EMS4, B3GZ05, B3QUT2, B4T750, B4TJR3, B4TWJ0, B5BGP5, B5EGX4, B5F7J9, B5FIR8, B5R0L2, B5RET7, B5YSV2, B6I1U3, B7LHT3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

58 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance34
Likely benign3
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

2096 predictions. Top by Δscore:

VariantEffectΔscore
1:182803686:C:Gacceptor_gain1.0000
1:182803687:A:AGacceptor_gain1.0000
1:182803688:T:Gacceptor_gain1.0000
1:182803696:A:AGacceptor_gain1.0000
1:182803697:G:GGacceptor_gain1.0000
1:182803697:GA:Gacceptor_gain1.0000
1:182814778:TAAA:Tacceptor_loss1.0000
1:182814779:A:AGacceptor_gain1.0000
1:182814779:AAAG:Aacceptor_gain1.0000
1:182814780:A:Gacceptor_gain1.0000
1:182814781:A:AGacceptor_gain1.0000
1:182814782:G:GGacceptor_gain1.0000
1:182814782:GGCCC:Gacceptor_gain1.0000
1:182814856:AAG:Adonor_gain1.0000
1:182814856:AAGGT:Adonor_loss1.0000
1:182814857:AG:Adonor_gain1.0000
1:182814857:AGGTA:Adonor_loss1.0000
1:182814858:GG:Gdonor_gain1.0000
1:182814858:GGTA:Gdonor_loss1.0000
1:182814859:G:GAdonor_loss1.0000
1:182814859:G:GGdonor_gain1.0000
1:182816803:AAGAG:Adonor_loss1.0000
1:182816804:AGA:Adonor_gain1.0000
1:182816805:GA:Gdonor_gain1.0000
1:182816805:GAG:Gdonor_gain1.0000
1:182816806:AGTA:Adonor_loss1.0000
1:182816807:G:GGdonor_gain1.0000
1:182816808:T:Adonor_loss1.0000
1:182818787:A:Gacceptor_gain1.0000
1:182825779:A:AGacceptor_gain1.0000

AlphaMissense

2097 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:182806210:T:AW70R0.997
1:182806210:T:CW70R0.997
1:182818603:T:CF174L0.997
1:182818605:C:AF174L0.997
1:182818605:C:GF174L0.997
1:182818606:A:CS175R0.997
1:182818608:T:AS175R0.997
1:182818608:T:GS175R0.997
1:182822124:C:AN221K0.997
1:182822124:C:GN221K0.997
1:182828746:A:CK267N0.997
1:182828746:A:TK267N0.997
1:182806190:G:CR63P0.996
1:182818602:A:CK173N0.995
1:182818602:A:TK173N0.995
1:182818685:A:TD201V0.995
1:182828745:A:TK267I0.995
1:182818858:A:CS218R0.994
1:182822115:T:AS218R0.994
1:182822115:T:GS218R0.994
1:182794412:C:AA14E0.993
1:182806201:G:CA67P0.993
1:182814792:G:CA100P0.993
1:182818684:G:CD201H0.993
1:182818685:A:CD201A0.993
1:182818856:G:AG217D0.993
1:182806145:T:AV48E0.992
1:182806189:C:AR63S0.992
1:182814819:G:CA109P0.992
1:182818679:G:AG199E0.992

dbSNP variants (sampled 300 via entrez): RS1000032560 (1:182798405 T>G), RS1000082819 (1:182807604 T>A,C), RS1000112665 (1:182791158 T>C), RS1000162585 (1:182788756 T>C), RS1000176560 (1:182791978 T>C), RS1000215918 (1:182788214 C>A), RS1000490152 (1:182795020 T>C), RS1000531507 (1:182826852 C>T), RS1000575940 (1:182820483 G>C,T), RS1000633234 (1:182799859 G>A), RS1000684806 (1:182827837 A>C), RS1000705448 (1:182814228 C>G), RS1000721914 (1:182806522 G>A), RS1000881048 (1:182799880 C>A,T), RS1001076226 (1:182820659 T>C)

Disease associations

OMIM: gene MIM:611412 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

StudyTraitp-value
GCST004403_7Bone fracture in osteoporosis7.000000e-06
GCST007565_110Morning person1.000000e-28
GCST012020_241Serum metabolite levels2.000000e-18

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0008328chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

49 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression8
Endosulfandecreases expression3
bisphenol Aincreases methylation, decreases expression, decreases methylation2
Cyclosporineincreases expression, decreases expression2
Cadmium Chloridedecreases expression, increases expression2
Particulate Matterdecreases expression2
2,4,6-tribromophenolincreases expression1
bufotalindecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
trichostatin Aincreases expression1
sodium bichromatedecreases expression1
butyraldehydeincreases expression1
tetrabromobisphenol Aincreases expression1
perfluorooctanoic acidincreases expression1
nickel sulfatedecreases expression1
pentanalincreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
entinostatincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
nutlin 3affects cotreatment, increases expression1
abrinedecreases expression1
dorsomorphinincreases expression, affects cotreatment1
bisphenol Sincreases methylation1
jinfukangaffects cotreatment, increases expression1
Temozolomideaffects response to substance1
Sunitinibdecreases expression1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_TA92HAP1 NPL (-) 1Cancer cell lineMale
CVCL_XR05HAP1 NPL (-) 2Cancer cell lineMale
CVCL_XR06HAP1 NPL (-) 3Cancer cell lineMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): bone fracture