GARIN3

Summary

GARIN3 (golgi associated RAB2 interactor family member 3, HGNC:28397) is a protein-coding gene on chromosome 5q33.3, encoding Golgi-associated RAB2 interactor protein 3 (Q8TC56). May be involved in RNA biogenesis.

Predicted to be involved in gene expression and vacuole organization. Predicted to act upstream of or within several processes, including acrosome assembly; binding activity of sperm to zona pellucida; and penetration of zona pellucida. Located in nucleus.

Source: NCBI Gene 153745 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 125 total
• MANE Select transcript: NM_130899

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28397
Approved symbol	GARIN3
Name	golgi associated RAB2 interactor family member 3
Location	5q33.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC26988, GARI-L3
Ensembl gene	ENSG00000170613
Ensembl biotype	protein_coding
OMIM	619883
Entrez	153745

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000302938

RefSeq mRNA: 1 — MANE Select: NM_130899 NM_130899

CCDS: CCDS4335

Canonical transcript exons

ENST00000302938 — 2 exons

Exon	Start	End
ENSE00001164915	157161846	157163658
ENSE00001164921	157165563	157166264

Expression profiles

Bgee: expression breadth broad, 16 present calls, max score 90.95.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0501 / max 41.4998, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
64513	0.0501	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.95	gold quality
sperm	CL:0000019	89.35	silver quality
left testis	UBERON:0004533	86.16	gold quality
right testis	UBERON:0004534	85.83	gold quality
testis	UBERON:0000473	83.26	gold quality
parotid gland	UBERON:0001831	62.60	gold quality
myocardium	UBERON:0002349	58.98	gold quality
vena cava	UBERON:0004087	57.64	gold quality
adult organism	UBERON:0007023	55.55	gold quality
cardia of stomach	UBERON:0001162	54.44	gold quality
trabecular bone tissue	UBERON:0002483	53.53	gold quality
lateral globus pallidus	UBERON:0002476	52.93	gold quality
oocyte	CL:0000023	49.29	gold quality
buccal mucosa cell	CL:0002336	47.80	gold quality
lower lobe of lung	UBERON:0008949	47.18	silver quality
trachea	UBERON:0003126	46.90	gold quality
vastus lateralis	UBERON:0001379	46.80	gold quality
quadriceps femoris	UBERON:0001377	46.65	gold quality
substantia nigra pars reticulata	UBERON:0001966	46.05	gold quality
lateral nuclear group of thalamus	UBERON:0002736	44.94	gold quality
body of tongue	UBERON:0011876	44.59	gold quality
layer of synovial tissue	UBERON:0007616	44.58	gold quality
pharyngeal mucosa	UBERON:0000355	43.83	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
subthalamic nucleus	UBERON:0001906	43.27	gold quality
epithelium of nasopharynx	UBERON:0001951	43.12	gold quality
tongue	UBERON:0001723	42.99	gold quality
nipple	UBERON:0002030	42.94	gold quality
globus pallidus	UBERON:0001875	42.81	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	42.65	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	784.98
E-ANND-3	no	2.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting GARIN3, 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-4795-3P	100.00	74.62	4024
HSA-MIR-17-3P	99.55	66.77	1311
HSA-MIR-4292	99.16	65.57	1767
HSA-MIR-6791-5P	99.16	65.92	1844
HSA-MIR-203B-3P	97.82	66.27	979
HSA-MIR-509-3-5P	97.21	67.74	1517
HSA-MIR-509-5P	97.21	67.90	1512
HSA-MIR-4418	97.04	67.16	1372
HSA-MIR-4653-3P	96.26	67.03	725

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Garin3	ENSMUSG00000020401
rattus_norvegicus	Garin3	ENSRNOG00000021425

Paralogs (7): GARIN1B (ENSG00000135248), GARIN5A (ENSG00000142530), GARIN4 (ENSG00000162771), GARIN2 (ENSG00000172717), GARIN5B (ENSG00000180043), GARIN6 (ENSG00000180219), GARIN1A (ENSG00000205085)

Protein

Protein identifiers

Golgi-associated RAB2 interactor protein 3 — Q8TC56 (reviewed: Q8TC56)

All UniProt accessions (2): Q8TC56, A0A140VJJ4

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in RNA biogenesis.

Subunit / interactions. Interacts (via N-terminus) with RAB2B (in GTP-bound form). Interacts with FRG1.

Subcellular location. Golgi apparatus. Nucleus. Cajal body.

Tissue specificity. Expressed in adult spermatocytes and spermatids (at protein level).

Similarity. Belongs to the GARIN family.

RefSeq proteins (1): NP_570969* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR022168	GARIL-like_Rab2B-bd	Domain

Pfam: PF12480

UniProt features (15 total): compositionally biased region 6, sequence variant 3, region of interest 2, chain 1, modified residue 1, sequence conflict 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TC56-F1	51.61	0.12

Functional residue map

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

Post-translational modifications (1): 592

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 89 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, GOBP_SINGLE_FERTILIZATION, GOBP_VESICLE_ORGANIZATION, GOBP_MALE_GAMETE_GENERATION, GOBP_SECRETORY_GRANULE_ORGANIZATION, GOBP_CELLULAR_COMPONENT_ASSEMBLY_INVOLVED_IN_MORPHOGENESIS, GOBP_CILIUM_MOVEMENT, GOBP_SPERM_EGG_RECOGNITION, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOBP_ACROSOME_ASSEMBLY, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_MULTI_MULTICELLULAR_ORGANISM_PROCESS, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION

GO Biological Process (7): cell morphogenesis (GO:0000902), acrosome assembly (GO:0001675), binding of sperm to zona pellucida (GO:0007339), penetration of zona pellucida (GO:0007341), flagellated sperm motility (GO:0030317), spermatid development (GO:0007286), single fertilization (GO:0007338)

GO Molecular Function (0):

GO Cellular Component (4): nucleus (GO:0005634), Golgi apparatus (GO:0005794), Cajal body (GO:0015030), sperm head (GO:0061827)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	2
anatomical structure morphogenesis	1
developmental process involved in reproduction	1
spermatid development	1
cellular component assembly involved in morphogenesis	1
cellular process involved in reproduction in multicellular organism	1
secretory granule organization	1
organelle assembly	1
sperm-egg recognition	1
single fertilization	1
multi-multicellular organism process	1
multicellular organismal reproductive process	1
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
germ cell development	1
spermatid differentiation	1
fertilization	1
cytoplasm	1
endomembrane system	1
nuclear ribonucleoprotein granule	1
cellular anatomical structure	1

Protein interactions and networks

STRING

374 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GARIN3	SPEM3	A0A1B0GUW6	576
GARIN3	SPATA31F1	Q6ZU69	539
GARIN3	MORN5	Q5VZ52	519
GARIN3	C6orf118	Q5T5N4	507
GARIN3	PPP1R2B	Q6NXS1	507
GARIN3	PROCA1	Q8NCQ7	463
GARIN3	SPATA3	Q8NHX4	447
GARIN3	OR10A4	Q9H209	431
GARIN3	NT5C1B	Q96P26	419
GARIN3	FRG1	Q14331	418
GARIN3	CCDC136	Q96JN2	414
GARIN3	ZNF75A	Q96N20	400
GARIN3	LELP1	Q5T871	392
GARIN3	ROPN1	Q9HAT0	389
GARIN3	TMEM202	A6NGA9	386

IntAct

2 interactions, top by confidence:

A	B	Type	Score
Prdm16	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (3): FAM71B (Affinity Capture-MS), FAM71B (Affinity Capture-MS), FAM71B (Affinity Capture-MS)

ESM2 similar proteins: A2ASS6, A8DYP0, E9QMW4, G4SLH0, J7M799, M9MRD1, O15061, O43491, O55103, O70318, O75952, O77788, P07197, P08553, P08855, P11799, P12839, P16053, P27321, P51125, P54938, P57786, P82179, P83741, Q06637, Q13061, Q23551, Q28820, Q4R3X7, Q63425, Q66H38, Q696W0, Q6TS35, Q70IV5, Q7Z589, Q7ZUV7, Q86TC9, Q8BMB0, Q8TC56, Q8WZ42

Diamond homologs: A1L3C1, B2RXB0, D3YV92, Q2KIP3, Q2YDE8, Q32L49, Q3UZD7, Q4R323, Q5STT6, Q66H38, Q68FV5, Q6IPT2, Q6NXP2, Q8IYT1, Q8N5Q1, Q8N9W8, Q8NEG0, Q8TC56, Q95K21, Q95K27, Q96KD3, Q5RJN7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	110
Likely benign	14
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

165 predictions. Top by Δscore:

Variant	Effect	Δscore
5:157163666:A:T	acceptor_gain	1.0000
5:157165562:CCA:C	donor_gain	1.0000
5:157163656:AGCCT:A	acceptor_gain	0.9900
5:157163658:CCTA:C	acceptor_gain	0.9900
5:157163665:C:CT	acceptor_gain	0.9900
5:157165556:GGCTT:G	donor_loss	0.9900
5:157165557:GCTT:G	donor_loss	0.9900
5:157165558:CTTAC:C	donor_loss	0.9900
5:157165559:TTA:T	donor_loss	0.9900
5:157165560:TA:T	donor_loss	0.9900
5:157165561:A:AC	donor_gain	0.9900
5:157165562:C:CA	donor_loss	0.9900
5:157165562:C:CC	donor_gain	0.9900
5:157163657:GC:G	acceptor_gain	0.9800
5:157163657:GCCT:G	acceptor_gain	0.9800
5:157163658:CC:C	acceptor_loss	0.9800
5:157163659:C:CC	acceptor_gain	0.9800
5:157163661:A:C	acceptor_gain	0.9800
5:157165684:T:TA	donor_gain	0.9800
5:157165685:C:A	donor_gain	0.9800
5:157163655:CAGC:C	acceptor_gain	0.9700
5:157163658:CCTAT:C	acceptor_gain	0.9700
5:157163665:C:T	acceptor_gain	0.9700
5:157164738:G:A	donor_gain	0.9700
5:157165562:CCACT:C	donor_gain	0.9700
5:157163654:GCAGC:G	acceptor_gain	0.9600
5:157163655:CAGCC:C	acceptor_gain	0.9600
5:157165562:C:CT	donor_gain	0.9600
5:157164746:G:C	donor_gain	0.9500
5:157163656:AGC:A	acceptor_gain	0.9400

AlphaMissense

3969 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:157165667:A:G	W168R	0.986
5:157165667:A:T	W168R	0.986
5:157165665:C:A	W168C	0.985
5:157165665:C:G	W168C	0.985
5:157166016:A:C	F51L	0.985
5:157166016:A:T	F51L	0.985
5:157166018:A:G	F51L	0.985
5:157165674:A:C	F165L	0.982
5:157165674:A:T	F165L	0.982
5:157165676:A:G	F165L	0.982
5:157165778:A:G	S131P	0.981
5:157165714:A:G	L152P	0.979
5:157165750:A:G	L140P	0.979
5:157165719:A:C	F150L	0.975
5:157165719:A:T	F150L	0.975
5:157165721:A:G	F150L	0.975
5:157166022:A:C	S49R	0.975
5:157166022:A:T	S49R	0.975
5:157166024:T:G	S49R	0.975
5:157165744:A:G	L142P	0.974
5:157165747:C:G	R141P	0.972
5:157165906:A:T	V88D	0.970
5:157166017:A:G	F51S	0.970
5:157165708:A:G	L154S	0.969
5:157165753:T:G	Q139P	0.969
5:157165726:C:G	R148P	0.965
5:157165675:A:C	F165C	0.959
5:157165780:A:G	I130T	0.958
5:157165780:A:C	I130S	0.957
5:157165666:C:G	W168S	0.955

dbSNP variants (sampled 300 via entrez): RS1000851871 (5:157167324 G>T), RS1000895882 (5:157167082 C>T), RS1001806042 (5:157162515 C>T), RS1002550966 (5:157166434 T>G), RS1002755969 (5:157163980 T>G), RS1003472073 (5:157163848 G>T), RS1004524530 (5:157161916 C>T), RS1004747499 (5:157163773 G>A), RS1004968515 (5:157167677 C>A,G), RS1005881468 (5:157164607 C>T), RS1006208712 (5:157164708 C>G), RS1006807968 (5:157166046 G>A,C,T), RS1007166525 (5:157166346 C>T), RS1007560461 (5:157161855 A>C), RS1007754139 (5:157167920 A>G)

Disease associations

OMIM: gene MIM:619883 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST003518_6	Daytime sleep phenotypes	7.000000e-06
GCST009597_71	Multiple sclerosis	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007828	daytime rest measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, decreases methylation	2
CGP 52608	affects binding, increases reaction	1
Resveratrol	decreases expression, affects cotreatment	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	decreases expression	1

Clinical trials (associated diseases)

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