NSG2

Summary

NSG2 (neuronal vesicle trafficking associated 2, HGNC:24955) is a protein-coding gene on chromosome 5q35.2, encoding Neuronal vesicle trafficking-associated protein 2 (Q9Y328).

Predicted to enable clathrin light chain binding activity. Predicted to be involved in clathrin coat assembly and endosomal transport. Located in Golgi apparatus.

Source: NCBI Gene 51617 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 28 total
• MANE Select transcript: NM_015980

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24955
Approved symbol	NSG2
Name	neuronal vesicle trafficking associated 2
Location	5q35.2
Locus type	gene with protein product
Status	Approved
Aliases	HMP19, CALY3
Ensembl gene	ENSG00000170091
Ensembl biotype	protein_coding
OMIM	616752
Entrez	51617

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 6 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000303177, ENST00000517587, ENST00000517902, ENST00000519717, ENST00000519867, ENST00000521146, ENST00000521278, ENST00000521585, ENST00000521959, ENST00000892999

RefSeq mRNA: 1 — MANE Select: NM_015980 NM_015980

CCDS: CCDS4391

Canonical transcript exons

ENST00000303177 — 5 exons

Exon	Start	End
ENSE00001903708	174107314	174109179
ENSE00002103964	174045706	174045843
ENSE00003493679	174104228	174104338
ENSE00003536944	174046734	174046884
ENSE00003649437	174064232	174064315

Expression profiles

Bgee: expression breadth ubiquitous, 179 present calls, max score 99.67.

FANTOM5 (CAGE): breadth broad, TPM avg 24.5171 / max 1396.8458, expressed in 247 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
60318	22.3672	241
60319	1.8778	162
60320	0.1587	74
60321	0.1134	54

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	99.67	gold quality
nucleus accumbens	UBERON:0001882	99.12	gold quality
ganglionic eminence	UBERON:0004023	99.02	gold quality
caudate nucleus	UBERON:0001873	98.73	gold quality
putamen	UBERON:0001874	98.48	gold quality
amygdala	UBERON:0001876	98.20	gold quality
right frontal lobe	UBERON:0002810	97.99	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	97.95	gold quality
anterior cingulate cortex	UBERON:0009835	97.93	gold quality
cingulate cortex	UBERON:0003027	97.89	gold quality
prefrontal cortex	UBERON:0000451	97.83	gold quality
hypothalamus	UBERON:0001898	97.66	gold quality
cerebellar cortex	UBERON:0002129	97.60	gold quality
cerebellar hemisphere	UBERON:0002245	97.60	gold quality
right hemisphere of cerebellum	UBERON:0014890	97.60	gold quality
frontal cortex	UBERON:0001870	97.58	gold quality
frontal lobe	UBERON:0016525	97.58	gold quality
neocortex	UBERON:0001950	97.45	gold quality
lateral globus pallidus	UBERON:0002476	97.45	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.43	gold quality
telencephalon	UBERON:0001893	97.42	gold quality
cerebral cortex	UBERON:0000956	97.33	gold quality
cerebellum	UBERON:0002037	97.21	gold quality
temporal lobe	UBERON:0001871	97.14	gold quality
lateral nuclear group of thalamus	UBERON:0002736	97.03	gold quality
Ammon’s horn	UBERON:0001954	96.79	gold quality
middle temporal gyrus	UBERON:0002771	96.71	gold quality
substantia nigra pars compacta	UBERON:0001965	96.69	gold quality
superior frontal gyrus	UBERON:0002661	96.48	gold quality
Brodmann (1909) area 46	UBERON:0006483	96.39	gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 9.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	2751.02
E-HCAD-5	yes	1170.60
E-MTAB-11121	yes	527.44
E-GEOD-75140	yes	273.74
E-GEOD-93593	yes	133.69
E-GEOD-84465	yes	24.86
E-ANND-3	yes	4.35
E-HCAD-10	yes	3.89
E-GEOD-83139	yes	3.81
E-MTAB-8894	no	813.04
E-MTAB-9154	no	793.36
E-ENAD-27	no	3.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

123 targeting NSG2, 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-MIR-340-5P	100.00	72.50	4437
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-1236-3P	99.94	68.04	1695

Literature-anchored findings (GeneRIF, showing 1)

• found in discrete punctae restricted to the somatodendritic arbors of developing mouse and human neurons, and a significant proportion of NSG2 punctae colocalize with postsynaptic HOMER1 and surface-expressed AMPA-type glutamate receptors (AMPARs) at excitatory synapses. (PMID:30680309)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	nsg2	ENSDARG00000102975
mus_musculus	Nsg2	ENSMUSG00000020297

Paralogs (2): CALY (ENSG00000130643), NSG1 (ENSG00000168824)

Protein

Protein identifiers

Neuronal vesicle trafficking-associated protein 2 — Q9Y328 (reviewed: Q9Y328)

Alternative names: Neuron-specific protein family member 2, Protein p19

All UniProt accessions (5): Q9Y328, E5RGE8, E5RH73, E5RHS6, G3XAM5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane. Golgi apparatus. trans-Golgi network membrane. Cell projection. Dendrite. Endosome membrane. Early endosome membrane. Late endosome membrane. Lysosome lumen. Cytoplasmic vesicle membrane. Golgi stack membrane. Endosome. Multivesicular body membrane.

Similarity. Belongs to the NSG family.

RefSeq proteins (1): NP_057064* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009431	NSG	Family

Pfam: PF06387

UniProt features (7 total): topological domain 2, chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y328-F1	58.61	0.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 285 (showing top): HNF3ALPHA_Q6, LFA1_Q6, GCANCTGNY_MYOD_Q6, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_CLATHRIN_COAT_ASSEMBLY, GOBP_VESICLE_MEDIATED_TRANSPORT, TAL1ALPHAE47_01, FOXO1_01, CAGCTG_AP4_Q5, GCGCTTT_MIR518B_MIR518C_MIR518D, AGCGCTT_MIR518F_MIR518E_MIR518A, GOCC_TRANS_GOLGI_NETWORK, MYOD_01, FREAC3_01, HEN1_01

GO Biological Process (3): endosomal transport (GO:0016197), clathrin coat assembly (GO:0048268), regulation of postsynaptic membrane neurotransmitter receptor levels (GO:0099072)

GO Molecular Function (2): clathrin light chain binding (GO:0032051), protein binding (GO:0005515)

GO Cellular Component (20): endosome (GO:0005768), early endosome (GO:0005769), late endosome (GO:0005770), Golgi apparatus (GO:0005794), membrane (GO:0016020), dendrite (GO:0030425), cytoplasmic vesicle membrane (GO:0030659), early endosome membrane (GO:0031901), multivesicular body membrane (GO:0032585), trans-Golgi network membrane (GO:0032588), lysosomal lumen (GO:0043202), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), Golgi cis cisterna membrane (GO:1990674), lysosome (GO:0005764), endosome membrane (GO:0010008), cytoplasmic vesicle (GO:0031410), late endosome membrane (GO:0031902), Golgi cisterna membrane (GO:0032580), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
endosome	3
endomembrane system	2
cytoplasmic vesicle	2
cytoplasm	2
cellular anatomical structure	2
endosome membrane	2
organelle membrane	2
vesicle-mediated transport	1
intracellular transport	1
protein-containing complex assembly	1
regulation of biological quality	1
clathrin binding	1
binding	1
intracellular membrane-bounded organelle	1
neuron projection	1
dendritic tree	1
vesicle membrane	1
early endosome	1
multivesicular body	1
late endosome membrane	1
trans-Golgi network	1
lysosome	1
vacuolar lumen	1
postsynaptic density	1
postsynaptic membrane	1
postsynaptic specialization membrane	1
synapse	1
Golgi cis cisterna	1
Golgi cisterna membrane	1
lytic vacuole	1
cytoplasmic vesicle membrane	1
bounding membrane of organelle	1
intracellular vesicle	1
late endosome	1
Golgi cisterna	1

Protein interactions and networks

STRING

468 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NSG2	CDC6	Q99741	547
NSG2	GRXCR2	A6NFK2	493
NSG2	PPP1R9B	Q96SB3	493
NSG2	LINGO2	Q7L985	415
NSG2	TRIM67	Q6ZTA4	406
NSG2	EMC4	Q5J8M3	397
NSG2	KIFAP3	Q92845	390
NSG2	CDKN2B	P42772	388
NSG2	ETS1	P14921	388
NSG2	FBXO25	Q8TCJ0	385
NSG2	STXBP5L	Q9Y2K9	384
NSG2	ETS2	P15036	383
NSG2	ID1	P41134	381
NSG2	XIAP	P98170	366
NSG2	SCG3	Q8WXD2	364

IntAct

33 interactions, top by confidence:

A	B	Type	Score
NSG2	HSPA5	psi-mi:“MI:0914”(association)	0.560
TTMP	NSG2	psi-mi:“MI:0915”(physical association)	0.560
CLEC7A	NSG2	psi-mi:“MI:0915”(physical association)	0.560
ANKRD46	NSG2	psi-mi:“MI:0915”(physical association)	0.560
RRH	NSG2	psi-mi:“MI:0915”(physical association)	0.560
NSG2	HSPA5	psi-mi:“MI:0915”(physical association)	0.560
NSG2	APOC1	psi-mi:“MI:0915”(physical association)	0.370
NSG2	ZNF768	psi-mi:“MI:0915”(physical association)	0.370
NSG2	NDUFA2	psi-mi:“MI:0915”(physical association)	0.370
NSG2	RPS27	psi-mi:“MI:0915”(physical association)	0.370
NSG2	SERPINH1	psi-mi:“MI:0915”(physical association)	0.370
NSG2	SUPT4H1	psi-mi:“MI:0915”(physical association)	0.370
NSG2	TNNT1	psi-mi:“MI:0915”(physical association)	0.370
TSPAN6	NSG2	psi-mi:“MI:0915”(physical association)	0.370
NSG2	UCHL3	psi-mi:“MI:0915”(physical association)	0.370
CACNA1C	SYT5	psi-mi:“MI:0914”(association)	0.350
HCN1	USP27X	psi-mi:“MI:0914”(association)	0.350
CACNA1C	IGLL5	psi-mi:“MI:0914”(association)	0.350
CACNA1C	CACNB4	psi-mi:“MI:0914”(association)	0.350
HCN1	POTEF	psi-mi:“MI:0914”(association)	0.350
CACNA1C	DISP2	psi-mi:“MI:0914”(association)	0.350
NSG2	APLP2	psi-mi:“MI:0914”(association)	0.350
TTMP	NSG2	psi-mi:“MI:0915”(physical association)	0.000
CLEC7A	NSG2	psi-mi:“MI:0915”(physical association)	0.000
ANKRD46	NSG2	psi-mi:“MI:0915”(physical association)	0.000
RRH	NSG2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (25): ECM1 (Affinity Capture-MS), ASAH1 (Affinity Capture-MS), HSPA5 (Affinity Capture-MS), SLC35F6 (Two-hybrid), HMP19 (Two-hybrid), CLEC7A (Two-hybrid), RRH (Two-hybrid), ANKRD46 (Two-hybrid), HSPA5 (Affinity Capture-MS), TMEM59 (Affinity Capture-MS), DNAJC16 (Affinity Capture-MS), ITFG1 (Affinity Capture-MS), CCDC51 (Affinity Capture-MS), ITM2B (Affinity Capture-MS), APLP2 (Affinity Capture-MS)

ESM2 similar proteins: A0A088MLT8, A2AQ25, A2BE76, B0R1D5, B3KU38, B5DF41, B5DGK1, E9PSK7, O15079, O55003, O60238, O60271, P47759, Q08CB3, Q0VCZ0, Q12983, Q14AM7, Q14CZ0, Q28HY5, Q32KN2, Q3KR51, Q3MHV6, Q3T013, Q3ZCD8, Q3ZK22, Q4KM98, Q4R8G4, Q58A65, Q5R795, Q5T5P2, Q5XI52, Q62739, Q62768, Q6DC60, Q6GQB5, Q6PAX8, Q6PCP5, Q6PFP3, Q7SZQ4, Q80U23

Diamond homologs: P02683, P42857, P47759, P58821, Q0VCZ0, Q3KR51, Q4R5Q3, Q5RF46, Q62092, Q8QFP1, Q9DCA7, Q9NYX4, Q9Y328

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	23
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

913 predictions. Top by Δscore:

Variant	Effect	Δscore
5:174045839:GCACA:G	donor_gain	1.0000
5:174045840:CACA:C	donor_gain	1.0000
5:174045842:CA:C	donor_gain	1.0000
5:174045843:AG:A	donor_loss	1.0000
5:174045844:G:GG	donor_gain	1.0000
5:174045844:GTAA:G	donor_loss	1.0000
5:174045848:G:GG	donor_gain	1.0000
5:174046882:AAGGT:A	donor_loss	1.0000
5:174046883:AGGTA:A	donor_loss	1.0000
5:174064226:TTTCA:T	acceptor_loss	1.0000
5:174064228:TCA:T	acceptor_loss	1.0000
5:174064229:CAG:C	acceptor_loss	1.0000
5:174064230:A:AG	acceptor_gain	1.0000
5:174064230:AGG:A	acceptor_loss	1.0000
5:174064230:AGGT:A	acceptor_gain	1.0000
5:174064231:G:GA	acceptor_loss	1.0000
5:174064231:G:GG	acceptor_gain	1.0000
5:174064231:GGT:G	acceptor_gain	1.0000
5:174064231:GGTG:G	acceptor_gain	1.0000
5:174064282:G:GT	donor_gain	1.0000
5:174064282:G:T	donor_gain	1.0000
5:174104334:ATAAG:A	donor_loss	1.0000
5:174104337:AGGT:A	donor_loss	1.0000
5:174104339:G:GA	donor_loss	1.0000
5:174104340:T:G	donor_loss	1.0000
5:174107312:A:AG	acceptor_gain	1.0000
5:174107313:G:GA	acceptor_gain	1.0000
5:174107313:GC:G	acceptor_gain	1.0000
5:174107313:GCA:G	acceptor_gain	1.0000
5:174107313:GCAC:G	acceptor_gain	1.0000

AlphaMissense

1110 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:174104267:T:C	C85R	1.000
5:174104315:T:C	C101R	1.000
5:174104316:G:A	C101Y	1.000
5:174104327:T:C	F105L	1.000
5:174104329:C:A	F105L	1.000
5:174104329:C:G	F105L	1.000
5:174107323:T:A	C112S	1.000
5:174107323:T:C	C112R	1.000
5:174107324:G:A	C112Y	1.000
5:174107324:G:C	C112S	1.000
5:174107325:T:G	C112W	1.000
5:174104243:A:C	S77R	0.999
5:174104245:C:A	S77R	0.999
5:174104245:C:G	S77R	0.999
5:174104250:C:A	A79D	0.999
5:174104253:T:C	L80P	0.999
5:174104256:C:A	A81D	0.999
5:174104258:T:C	F82L	0.999
5:174104260:C:A	F82L	0.999
5:174104260:C:G	F82L	0.999
5:174104262:T:A	L83H	0.999
5:174104262:T:C	L83P	0.999
5:174104262:T:G	L83R	0.999
5:174104280:T:A	L89Q	0.999
5:174104280:T:C	L89P	0.999
5:174104280:T:G	L89R	0.999
5:174104286:T:A	V91D	0.999
5:174104293:A:C	K93N	0.999
5:174104293:A:T	K93N	0.999
5:174104315:T:A	C101S	0.999

dbSNP variants (sampled 300 via entrez): RS1000007583 (5:174049708 C>G), RS1000025884 (5:174076022 A>G), RS1000026386 (5:174047040 A>G), RS1000040007 (5:174053201 C>T), RS1000150887 (5:174096933 G>A), RS1000219181 (5:174072742 G>A), RS1000250548 (5:174072444 C>A,G,T), RS1000281970 (5:174077111 G>A), RS1000352032 (5:174077442 T>G), RS1000385813 (5:174059842 C>A), RS1000461561 (5:174047413 T>C), RS1000492072 (5:174060513 G>A), RS1000507977 (5:174054055 G>C,T), RS1000580854 (5:174100916 G>A,T), RS1000607721 (5:174060323 A>T)

Disease associations

OMIM: gene MIM:616752 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST001521_24	Subcutaneous adipose tissue	7.000000e-06
GCST002003_5	Adverse response to chemotherapy (neutropenia/leucopenia) (gemcitabine)	7.000000e-06
GCST006988_74	Blond vs. brown/black hair color	1.000000e-09
GCST007576_155	Chronotype	2.000000e-10
GCST007637_48	Diffusing capacity of carbon monoxide	2.000000e-06
GCST009391_1035	Metabolite levels	4.000000e-06
GCST009391_532	Metabolite levels	2.000000e-06
GCST009391_913	Metabolite levels	7.000000e-06
GCST011696_12	Alzheimer’s disease	2.000000e-06
GCST90020025_980	Waist-to-hip ratio adjusted for BMI	6.000000e-09
GCST90020027_709	Waist-hip index	2.000000e-09

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0003924	hair color
EFO:0008328	chronotype measurement
EFO:0009369	diffusing capacity of the lung for carbon monoxide
EFO:0009775	threonine measurement
EFO:0010528	quinolinic acid measurement
EFO:0010442	triacylglycerol 58:8 measurement
EFO:0007788	BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases expression	2
uranyl acetate	affects expression	1
(+)-JQ1 compound	decreases expression	1
Benzo(a)pyrene	increases expression	1
Doxorubicin	affects response to substance	1
Tretinoin	affects cotreatment, increases expression	1
Uranium	affects expression	1
Valproic Acid	decreases methylation	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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