ASNSD1

Summary

ASNSD1 (asparagine synthetase domain containing 1, HGNC:24910) is a protein-coding gene on chromosome 2q32.2, encoding Asparagine synthetase domain-containing protein 1 (Q9NWL6).

Predicted to enable asparagine synthase (glutamine-hydrolyzing) activity. Predicted to be involved in asparagine biosynthetic process. Predicted to act upstream of or within adipose tissue development; skeletal muscle tissue development; and transdifferentiation.

Source: NCBI Gene 54529 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 73 total
• MANE Select transcript: NM_019048

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24910
Approved symbol	ASNSD1
Name	asparagine synthetase domain containing 1
Location	2q32.2
Locus type	gene with protein product
Status	Approved
Aliases	NS3TP1, FLJ20752, NBLA00058
Ensembl gene	ENSG00000138381
Ensembl biotype	protein_coding
OMIM	619739
Entrez	54529

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000260952, ENST00000420250, ENST00000425590, ENST00000607062

RefSeq mRNA: 2 — MANE Select: NM_019048 NM_001353497, NM_019048

CCDS: CCDS2300

Canonical transcript exons

ENST00000260952 — 6 exons

Exon	Start	End
ENSE00000783862	189667764	189667945
ENSE00000883215	189666041	189667596
ENSE00000883216	189670441	189670831
ENSE00001001142	189663901	189663954
ENSE00001001143	189665376	189665451
ENSE00001705427	189661459	189661610

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 95.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 43.9803 / max 686.9537, expressed in 1801 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
24252	43.9803	1801

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	95.55	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	95.34	gold quality
biceps brachii	UBERON:0001507	95.33	gold quality
parietal pleura	UBERON:0002400	95.18	gold quality
pleura	UBERON:0000977	94.63	gold quality
tibia	UBERON:0000979	94.62	gold quality
ganglionic eminence	UBERON:0004023	94.36	gold quality
visceral pleura	UBERON:0002401	94.32	gold quality
ventricular zone	UBERON:0003053	94.10	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	94.00	gold quality
gastrocnemius	UBERON:0001388	93.94	gold quality
muscle of leg	UBERON:0001383	93.82	gold quality
skeletal muscle organ	UBERON:0014892	93.62	gold quality
muscle organ	UBERON:0001630	93.61	gold quality
germinal epithelium of ovary	UBERON:0001304	93.43	gold quality
islet of Langerhans	UBERON:0000006	93.32	gold quality
pigmented layer of retina	UBERON:0001782	93.30	gold quality
retina	UBERON:0000966	93.27	gold quality
deltoid	UBERON:0001476	93.26	gold quality
endothelial cell	CL:0000115	93.20	gold quality
vastus lateralis	UBERON:0001379	93.14	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.14	gold quality
eye	UBERON:0000970	93.12	gold quality
choroid plexus epithelium	UBERON:0003911	93.12	gold quality
palpebral conjunctiva	UBERON:0001812	93.07	gold quality
quadriceps femoris	UBERON:0001377	92.98	gold quality
skeletal muscle tissue	UBERON:0001134	92.88	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	92.77	gold quality
cerebellar vermis	UBERON:0004720	92.49	gold quality
embryo	UBERON:0000922	92.42	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting ASNSD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948

Literature-anchored findings (GeneRIF, showing 1)

• Normal human HL-7702 hepatocytes can efficiently express specific HCV NS3 protein in vitro. (PMID:16534843)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	asnsd1	ENSDARG00000000540
mus_musculus	Asnsd1	ENSMUSG00000026095
rattus_norvegicus	Asnsd1	ENSRNOG00000003942
drosophila_melanogaster	CG17486	FBGN0032997
caenorhabditis_elegans		WBGENE00010889

Paralogs (1): ASNS (ENSG00000070669)

Protein

Protein identifiers

Asparagine synthetase domain-containing protein 1 — Q9NWL6 (reviewed: Q9NWL6)

Alternative names: HCV NS3-transactivated protein 1

All UniProt accessions (4): C9IYZ1, C9J6C1, Q9NWL6, U3KQK8

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NWL6-1	1	yes
L0R819-1	2, uORF

RefSeq proteins (2): NP_001340426, NP_061921* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001962	Asn_synthase	Domain
IPR014729	Rossmann-like_a/b/a_fold	Homologous_superfamily
IPR017932	GATase_2_dom	Domain
IPR029055	Ntn_hydrolases_N	Homologous_superfamily
IPR051857	Asn_synthetase_domain	Family

Pfam: PF00733

UniProt features (7 total): domain 2, sequence variant 2, initiator methionine 1, chain 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NWL6-F1	85.95	0.72

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 (1): 2 (for gatase activity)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 124 (showing top): GOBP_MUSCLE_TISSUE_DEVELOPMENT, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_AMINO_ACID_BIOSYNTHETIC_PROCESS, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_SKELETAL_MUSCLE_ORGAN_DEVELOPMENT, GARY_CD5_TARGETS_DN, GOMF_LIGASE_ACTIVITY_FORMING_CARBON_NITROGEN_BONDS, GOBP_CONNECTIVE_TISSUE_DEVELOPMENT, BRACHAT_RESPONSE_TO_CISPLATIN, GOBP_ADIPOSE_TISSUE_DEVELOPMENT, GOMF_CARBON_NITROGEN_LIGASE_ACTIVITY_WITH_GLUTAMINE_AS_AMIDO_N_DONOR, COLINA_TARGETS_OF_4EBP1_AND_4EBP2, JOHNSTONE_PARVB_TARGETS_3_DN, LINSLEY_MIR16_TARGETS

GO Biological Process (8): obsolete asparagine biosynthetic process (GO:0006529), skeletal muscle tissue development (GO:0007519), transdifferentiation (GO:0060290), adipose tissue development (GO:0060612), muscle organ development (GO:0007517), biological_process (GO:0008150), amino acid biosynthetic process (GO:0008652), skeletal muscle organ development (GO:0060538)

GO Molecular Function (2): asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066), molecular_function (GO:0003674)

GO Cellular Component (1): cellular_component (GO:0005575)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
animal organ development	2
striated muscle tissue development	1
skeletal muscle organ development	1
cell differentiation	1
connective tissue development	1
muscle structure development	1
amino acid metabolic process	1
biosynthetic process	1
muscle organ development	1
carbon-nitrogen ligase activity, with glutamine as amido-N-donor	1

Protein interactions and networks

STRING

1547 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ASNSD1	TZMP1	A0A1B0GUW7	782
ASNSD1	ASDURF	L0R819	779
ASNSD1	TCF15	Q12870	371
ASNSD1	MYMX	A0A1B0GTQ4	359
ASNSD1	ALDH18A1	P54886	353
ASNSD1	ASNS	P08184	348
ASNSD1	MIA2	Q96PC5	328
ASNSD1	DGKK	Q5KSL6	323
ASNSD1	GMPS	P49915	308
ASNSD1	H6PD	O95479	306
ASNSD1	AMTN	Q6UX39	305
ASNSD1	YARS1	P54577	304
ASNSD1	NEIL1	Q96FI4	299
ASNSD1	TMEM109	Q9BVC6	296
ASNSD1	PPAT	Q06203	295

IntAct

131 interactions, top by confidence:

A	B	Type	Score
PTPRA	LGALS1	psi-mi:“MI:0914”(association)	0.640
SCRIB	ASNSD1	psi-mi:“MI:0407”(direct interaction)	0.620
SNTB1	ASNSD1	psi-mi:“MI:0407”(direct interaction)	0.620
ASNSD1	SNTB1	psi-mi:“MI:0407”(direct interaction)	0.620
ASNSD1	SCRIB	psi-mi:“MI:0407”(direct interaction)	0.620
ASNSD1	PDZK1	psi-mi:“MI:0407”(direct interaction)	0.590
RFPL3	RFPL1	psi-mi:“MI:0914”(association)	0.530
ASNSD1	SNX27	psi-mi:“MI:0407”(direct interaction)	0.440
ASNSD1	MAST2	psi-mi:“MI:0407”(direct interaction)	0.440
PTPN3	ASNSD1	psi-mi:“MI:0407”(direct interaction)	0.440
SNTG2	ASNSD1	psi-mi:“MI:0407”(direct interaction)	0.440
SNTA1	ASNSD1	psi-mi:“MI:0407”(direct interaction)	0.440
ASNSD1	PDZRN4	psi-mi:“MI:0407”(direct interaction)	0.440
ASNSD1	NHERF2	psi-mi:“MI:0407”(direct interaction)	0.440
RHPN1	ASNSD1	psi-mi:“MI:0407”(direct interaction)	0.440
ASNSD1	MAST1	psi-mi:“MI:0407”(direct interaction)	0.440
ASNSD1	PDZD7	psi-mi:“MI:0407”(direct interaction)	0.440
ASNSD1	PDZRN3	psi-mi:“MI:0407”(direct interaction)	0.440
ASNSD1	SHANK1	psi-mi:“MI:0407”(direct interaction)	0.440
ASNSD1	LIN7B	psi-mi:“MI:0407”(direct interaction)	0.440
ASNSD1	ARHGEF12	psi-mi:“MI:0407”(direct interaction)	0.440
WHRN	ASNSD1	psi-mi:“MI:0407”(direct interaction)	0.440
ASNSD1	FRMPD4	psi-mi:“MI:0407”(direct interaction)	0.440
ASNSD1	GRID2IP	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (34): ASNSD1 (Affinity Capture-MS), ASNSD1 (Affinity Capture-MS), ASNSD1 (Affinity Capture-MS), ASNSD1 (Affinity Capture-MS), ASNSD1 (Affinity Capture-MS), ASNSD1 (Affinity Capture-MS), ASNSD1 (Affinity Capture-MS), ASNSD1 (Negative Genetic), ASNSD1 (Affinity Capture-MS), ASNSD1 (Affinity Capture-MS), ASNSD1 (Affinity Capture-MS), ASNSD1 (Affinity Capture-MS), ASNSD1 (Affinity Capture-MS), ASNSD1 (Proximity Label-MS), ASNSD1 (Affinity Capture-MS)

ESM2 similar proteins: B4KIW3, O14353, O24338, O24661, O74397, O74841, O94636, P19251, P19252, P23060, P24521, P31752, P38913, P40389, P43122, P48445, P49078, P49090, P49091, P49092, P49093, P49094, P53095, P78753, P87241, Q04489, Q08282, Q0V8E4, Q10313, Q10441, Q12093, Q12429, Q22017, Q43011, Q4R5D4, Q54MB4, Q5LJP9, Q5UQE1, Q5ZJN0, Q6C3P4

Diamond homologs: O74397, Q04489, Q0V8E4, Q4R5D4, Q5LJP9, Q5ZJN0, Q8BFS9, Q8JFW1, Q9NWL6, Q58516, F9VPA4, O24338, O57981, P49078, P49088, P54420, P59362, P78753, Q10MX3, Q43011, Q4J6D9, Q54MB4, Q56213, Q58456, Q58815, Q61024, Q6LWM9, Q72HF4, Q72V57, Q890U2, Q8EZQ1, Q8U4D1, Q8ZTZ0, Q9LFU1, Q9LV77

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 88 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Dopamine Neurotransmitter Release Cycle	5	45.1×	3e-06
Assembly and cell surface presentation of NMDA receptors	9	41.5×	5e-11
Neurexins and neuroligins	10	35.8×	2e-11
Protein-protein interactions at synapses	7	33.8×	8e-08
RHOA GTPase cycle	5	6.8×	6e-03
Neuronal System	7	5.6×	2e-03
Signaling by Rho GTPases	8	5.0×	2e-03
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	8	4.9×	2e-03

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	8	55.3×	6e-10
protein localization to synapse	5	45.6×	6e-06
receptor clustering	6	44.6×	5e-07
regulation of postsynaptic membrane neurotransmitter receptor levels	5	29.5×	5e-05
protein-containing complex assembly	10	13.6×	5e-07
cell-cell adhesion	10	12.1×	1e-06
regulation of small GTPase mediated signal transduction	5	8.6×	6e-03
protein localization to plasma membrane	6	7.8×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	65
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

651 predictions. Top by Δscore:

Variant	Effect	Δscore
2:189661606:GCAAG:G	donor_gain	1.0000
2:189661611:G:GG	donor_gain	1.0000
2:189661611:GT:G	donor_loss	1.0000
2:189661612:T:G	donor_loss	1.0000
2:189663789:G:GG	donor_gain	1.0000
2:189665450:GA:G	donor_gain	1.0000
2:189665452:G:GG	donor_gain	1.0000
2:189667941:GCAAG:G	donor_gain	1.0000
2:189667943:AAG:A	donor_loss	1.0000
2:189667944:AGG:A	donor_loss	1.0000
2:189667945:GGTAA:G	donor_loss	1.0000
2:189661596:GATC:G	donor_gain	0.9900
2:189661609:AG:A	donor_gain	0.9900
2:189661610:GG:G	donor_gain	0.9900
2:189663952:AGGGT:A	donor_loss	0.9900
2:189663953:GG:G	donor_gain	0.9900
2:189663954:GG:G	donor_gain	0.9900
2:189663954:GGT:G	donor_loss	0.9900
2:189663955:G:GT	donor_loss	0.9900
2:189663956:TGAG:T	donor_loss	0.9900
2:189663957:GAGT:G	donor_loss	0.9900
2:189665447:CAAGA:C	donor_gain	0.9900
2:189665448:AAGA:A	donor_gain	0.9900
2:189665449:AGA:A	donor_gain	0.9900
2:189665450:GAG:G	donor_gain	0.9900
2:189665451:AG:A	donor_loss	0.9900
2:189665454:AA:A	donor_loss	0.9900
2:189667763:GGTA:G	acceptor_gain	0.9900
2:189667946:G:GG	donor_gain	0.9900
2:189670435:TTTTA:T	acceptor_loss	0.9900

AlphaMissense

4230 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:189667184:T:C	L351P	0.997
2:189670610:T:C	F606L	0.997
2:189670612:T:A	F606L	0.997
2:189670612:T:G	F606L	0.997
2:189666551:G:C	R140P	0.996
2:189666556:A:C	S142R	0.996
2:189666558:C:A	S142R	0.996
2:189666558:C:G	S142R	0.996
2:189670596:A:T	K601I	0.996
2:189667405:T:A	W425R	0.995
2:189667405:T:C	W425R	0.995
2:189667789:A:T	D497V	0.995
2:189667792:A:T	E498V	0.995
2:189667898:T:A	N533K	0.995
2:189667898:T:G	N533K	0.995
2:189667905:C:A	R536S	0.995
2:189667916:A:C	R539S	0.995
2:189667916:A:T	R539S	0.995
2:189670597:A:C	K601N	0.995
2:189670597:A:T	K601N	0.995
2:189666355:T:A	W75R	0.994
2:189666355:T:C	W75R	0.994
2:189666550:C:A	R140S	0.994
2:189667789:A:C	D497A	0.994
2:189667793:G:C	E498D	0.994
2:189667793:G:T	E498D	0.994
2:189667906:G:C	R536P	0.994
2:189670536:A:T	K581I	0.994
2:189667507:A:C	S459R	0.993
2:189667509:C:A	S459R	0.993

dbSNP variants (sampled 300 via entrez): RS1000015422 (2:189662949 A>C), RS1000087038 (2:189663243 T>A,C), RS1000359822 (2:189669463 T>C), RS1000529587 (2:189664746 C>A), RS1001810915 (2:189660762 A>G), RS1001933550 (2:189665925 T>C), RS1002074869 (2:189660462 G>A), RS1002091032 (2:189660663 G>A), RS1002571912 (2:189663347 G>A), RS1002603037 (2:189663195 C>G), RS1002767503 (2:189671228 G>A), RS1002960988 (2:189664970 T>C), RS1003169423 (2:189670127 G>A), RS1003314703 (2:189664685 G>A,T), RS1003772981 (2:189669519 G>A)

Disease associations

OMIM: gene MIM:619739 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST90016674_22	Liver iron content	4.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance	3
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, decreases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression, increases expression	2
dicrotophos	decreases expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
bisphenol A	increases expression	1
kojic acid	decreases expression	1
methacrylaldehyde	increases oxidation, increases abundance, affects cotreatment	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
jinfukang	decreases expression	1
Sunitinib	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Arsenic	increases abundance, decreases expression	1
Calcitriol	decreases expression, affects cotreatment	1
Ozone	increases abundance, affects cotreatment, increases oxidation	1
Testosterone	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Valproic Acid	decreases methylation, increases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation	1
Lactic Acid	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1
Volatile Organic Compounds	affects cotreatment, increases oxidation	1

Clinical trials (associated diseases)

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