GARIN5A

Summary

GARIN5A (golgi associated RAB2 interactor 5A, HGNC:25107) is a protein-coding gene on chromosome 19q13.33, encoding Golgi-associated RAB2 interactor protein 5A (Q6IPT2). RAB2B effector protein which promotes cytosolic DNA-induced innate immune responses.

Predicted to be involved in defense response to virus; innate immune response; and positive regulation of type I interferon production. Predicted to act upstream of or within several processes, including flagellated sperm motility; penetration of zona pellucida; and spermatid development. Predicted to be located in Golgi apparatus. Predicted to be active in sperm head.

Source: NCBI Gene 112703 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 58 total — 1 pathogenic
• MANE Select transcript: NM_001308429

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25107
Approved symbol	GARIN5A
Name	golgi associated RAB2 interactor 5A
Location	19q13.33
Locus type	gene with protein product
Status	Approved
Aliases	GARIL5
Ensembl gene	ENSG00000142530
Ensembl biotype	protein_coding
OMIM	619890
Entrez	112703

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 non_stop_decay, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000593796, ENST00000595790, ENST00000599206, ENST00000600100, ENST00000600330, ENST00000602178, ENST00000897782, ENST00000897783, ENST00000953416

RefSeq mRNA: 2 — MANE Select: NM_001308429 NM_001308429, NM_138411

CCDS: CCDS33081, CCDS77337

Canonical transcript exons

ENST00000600100 — 5 exons

Exon	Start	End
ENSE00000954747	50475833	50475933
ENSE00001281799	50467622	50467829
ENSE00001354162	50475325	50475503
ENSE00003140527	50476130	50476848
ENSE00003518107	50466788	50466955

Expression profiles

Bgee: expression breadth ubiquitous, 179 present calls, max score 97.31.

FANTOM5 (CAGE): breadth broad, TPM avg 3.0999 / max 214.7165, expressed in 811 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182159	1.4327	338
182161	1.2502	594
182162	0.4068	236
182160	0.0102	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	97.31	gold quality
right testis	UBERON:0004534	97.18	gold quality
testis	UBERON:0000473	94.61	gold quality
sperm	CL:0000019	92.54	gold quality
oocyte	CL:0000023	90.66	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.39	gold quality
adult organism	UBERON:0007023	87.01	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.43	gold quality
secondary oocyte	CL:0000655	85.51	gold quality
prefrontal cortex	UBERON:0000451	83.84	gold quality
endothelial cell	CL:0000115	82.13	silver quality
hypothalamus	UBERON:0001898	81.06	gold quality
anterior cingulate cortex	UBERON:0009835	80.18	gold quality
caudate nucleus	UBERON:0001873	79.62	gold quality
right frontal lobe	UBERON:0002810	79.57	gold quality
putamen	UBERON:0001874	79.46	gold quality
frontal cortex	UBERON:0001870	78.93	gold quality
neocortex	UBERON:0001950	78.47	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	78.26	gold quality
nucleus accumbens	UBERON:0001882	78.04	gold quality
substantia nigra	UBERON:0002038	77.62	gold quality
Brodmann (1909) area 9	UBERON:0013540	77.50	gold quality
amygdala	UBERON:0001876	76.75	gold quality
cerebral cortex	UBERON:0000956	75.89	gold quality
hindlimb stylopod muscle	UBERON:0004252	75.84	gold quality
forebrain	UBERON:0001890	75.45	gold quality
primary visual cortex	UBERON:0002436	75.20	gold quality
midbrain	UBERON:0001891	75.07	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	74.82	gold quality
brain	UBERON:0000955	74.69	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	1728.67
E-ANND-3	no	2.38

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting GARIN5A, 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-7152-3P	99.97	67.47	849
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-889-3P	99.40	69.76	2103
HSA-MIR-6809-5P	99.13	68.45	1223
HSA-MIR-2355-5P	98.83	65.51	1589
HSA-MIR-3663-5P	97.01	64.84	713
HSA-MIR-6759-3P	96.94	68.31	823
HSA-MIR-1269A	92.75	64.61	542
HSA-MIR-1269B	92.75	64.73	538

Literature-anchored findings (GeneRIF, showing 1)

• The RAB2B-GARIL5 complex promotes cytosolic DNA-induced innate immune responses (Golgi-associated Rab2B interactor-like 5 = GARIL5, also known as FAM71E1) (PMID:28930687)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Garin5a	ENSMUSG00000051113
rattus_norvegicus	Garin5a	ENSRNOG00000031739

Paralogs (7): GARIN1B (ENSG00000135248), GARIN4 (ENSG00000162771), GARIN3 (ENSG00000170613), GARIN2 (ENSG00000172717), GARIN5B (ENSG00000180043), GARIN6 (ENSG00000180219), GARIN1A (ENSG00000205085)

Protein

Protein identifiers

Golgi-associated RAB2 interactor protein 5A — Q6IPT2 (reviewed: Q6IPT2)

All UniProt accessions (4): Q6IPT2, A0A075B789, A0A075B7A4, B3KWT0

UniProt curated annotations — full annotation on UniProt →

Function. RAB2B effector protein which promotes cytosolic DNA-induced innate immune responses. Regulates IFN responses against DNA viruses by regulating the CGAS-STING signaling axis.

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

Subcellular location. Golgi apparatus.

Similarity. Belongs to the GARIN family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6IPT2-1	1	yes
Q6IPT2-2	2

RefSeq proteins (2): NP_001295358, NP_612420 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR022168	GARIL-like_Rab2B-bd	Domain

Pfam: PF12480

UniProt features (6 total): region of interest 2, chain 1, compositionally biased region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6IPT2-F1	65.94	0.18

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 58 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, GOBP_POSITIVE_REGULATION_OF_TYPE_I_INTERFERON_PRODUCTION, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_CYTOKINE_PRODUCTION, RICKMAN_HEAD_AND_NECK_CANCER_A, GOBP_DEFENSE_RESPONSE_TO_VIRUS, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, GOBP_RESPONSE_TO_VIRUS, GOBP_POSITIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GEORGES_TARGETS_OF_MIR192_AND_MIR215, LU_EZH2_TARGETS_UP, GOBP_TYPE_I_INTERFERON_PRODUCTION, PEDRIOLI_MIR31_TARGETS_UP, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY

GO Biological Process (3): positive regulation of type I interferon production (GO:0032481), innate immune response (GO:0045087), defense response to virus (GO:0051607)

GO Molecular Function (0):

GO Cellular Component (1): Golgi apparatus (GO:0005794)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
positive regulation of cytokine production	1
regulation of type I interferon production	1
type I interferon production	1
immune response	1
defense response to symbiont	1
defense response	1
response to virus	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

222 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GARIN5A	TMEM89	A2RUT3	608
GARIN5A	FOXL2NB	Q6ZUU3	578
GARIN5A	OR4F21	O95013	573
GARIN5A	ZNF487	B1APH4	570
GARIN5A	EMC10	Q5UCC4	566
GARIN5A	PDHA2	P29803	542
GARIN5A	SLC5A9	Q2M3M2	533
GARIN5A	MORN5	Q5VZ52	519
GARIN5A	CCER1	Q8TC90	507
GARIN5A	CIMIP4	O43247	506
GARIN5A	EFCC1	Q9HA90	480
GARIN5A	ZNF853	P0CG23	477
GARIN5A	ZNF529	Q6P280	477
GARIN5A	PABPC3	Q9H361	453
GARIN5A	CLIP4	Q8N3C7	447
GARIN5A	RNF208	Q9H0X6	447

IntAct

2 interactions, top by confidence:

A	B	Type	Score
GARIN5A	PTPN11	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (3): FAM71E1 (Two-hybrid), FAM71E1 (Synthetic Lethality), FAM71E1 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A0U1RR11, A0A0U1RRI6, A6NCS6, A6NJG2, B0BN44, D3YXK1, E9PY61, E9Q0B3, F5H4A9, O00220, O00221, P09038, P0DPI3, P22083, P98077, Q08AU9, Q2M2W7, Q2M3V2, Q2TBI2, Q5F267, Q5FW56, Q5IS69, Q5R866, Q5T4W7, Q5TM52, Q5U4P2, Q5VTJ3, Q659K9, Q673H1, Q69ZB3, Q6AYE8, Q6IPT2, Q6PJ61, Q7RTU4, Q7TSX9, Q7YR31, Q80SU3, Q86SH2, Q86Y97, Q8NBR0

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

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	51
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1704220	NM_206538.4(EMC10):c.66del (p.Ser23fs)	Pathogenic

SpliceAI

771 predictions. Top by Δscore:

Variant	Effect	Δscore
19:50467611:T:TA	donor_gain	1.0000
19:50467627:A:AC	donor_gain	1.0000
19:50467627:ACT:A	donor_gain	1.0000
19:50467628:C:CC	donor_gain	1.0000
19:50467628:CT:C	donor_gain	1.0000
19:50467628:CTC:C	donor_gain	1.0000
19:50467630:C:CA	donor_gain	1.0000
19:50467825:ACAGC:A	acceptor_gain	1.0000
19:50467826:CAGC:C	acceptor_gain	1.0000
19:50467826:CAGCC:C	acceptor_gain	1.0000
19:50467830:C:CC	acceptor_gain	1.0000
19:50467830:CTGG:C	acceptor_loss	1.0000
19:50475827:CCCTA:C	donor_loss	1.0000
19:50475828:CCTAC:C	donor_loss	1.0000
19:50475829:CTA:C	donor_loss	1.0000
19:50475830:TAC:T	donor_loss	1.0000
19:50475831:A:C	donor_loss	1.0000
19:50476656:GGG:G	donor_gain	1.0000
19:50476657:GGG:G	donor_gain	1.0000
19:50466956:C:CC	acceptor_gain	0.9900
19:50467629:T:TA	donor_gain	0.9900
19:50467827:AGC:A	acceptor_gain	0.9900
19:50467828:GC:G	acceptor_gain	0.9900
19:50467829:CC:C	acceptor_gain	0.9900
19:50467834:G:GC	acceptor_gain	0.9900
19:50475320:GTTA:G	donor_loss	0.9900
19:50475321:TTA:T	donor_loss	0.9900
19:50475322:TACCC:T	donor_loss	0.9900
19:50475323:A:AC	donor_gain	0.9900
19:50475323:A:T	donor_loss	0.9900

AlphaMissense

1585 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:50467697:G:C	F224L	0.992
19:50467697:G:T	F224L	0.992
19:50467699:A:G	F224L	0.992
19:50475839:G:C	F118L	0.988
19:50475839:G:T	F118L	0.988
19:50475841:A:G	F118L	0.988
19:50467742:G:C	F209L	0.983
19:50467742:G:T	F209L	0.983
19:50467744:A:G	F209L	0.983
19:50467688:C:A	W227C	0.982
19:50467688:C:G	W227C	0.982
19:50475878:G:C	F105L	0.981
19:50475878:G:T	F105L	0.981
19:50475880:A:G	F105L	0.981
19:50467690:A:G	W227R	0.978
19:50467690:A:T	W227R	0.978
19:50475373:A:G	L164S	0.976
19:50475851:A:C	F114L	0.973
19:50475851:A:T	F114L	0.973
19:50475853:A:G	F114L	0.973
19:50467737:A:G	L211S	0.966
19:50475845:G:C	S116R	0.966
19:50475845:G:T	S116R	0.966
19:50475847:T:G	S116R	0.966
19:50467698:A:C	F224C	0.965
19:50467811:G:C	F186L	0.962
19:50467811:G:T	F186L	0.962
19:50467813:A:G	F186L	0.962
19:50475840:A:C	F118C	0.962
19:50475840:A:G	F118S	0.958

dbSNP variants (sampled 300 via entrez): RS1000417345 (19:50470242 G>A), RS1000510696 (19:50470462 A>G), RS1000803983 (19:50474464 G>C), RS1000897156 (19:50472635 G>A,T), RS1001182839 (19:50478010 G>A), RS1001807964 (19:50473665 C>G), RS1001860376 (19:50473931 G>A,C), RS1001923836 (19:50469772 A>G), RS1002376196 (19:50469980 C>T), RS1002516603 (19:50468015 A>G,T), RS1002715480 (19:50477833 C>T), RS1002715482 (19:50475733 C>A,T), RS1002975971 (19:50468897 G>A), RS1003342343 (19:50468735 C>T), RS1003429234 (19:50466760 G>A)

Disease associations

OMIM: gene MIM:619890 | disease phenotypes: MIM:619264

GenCC curated gene-disease

Mondo (1): neurodevelopmental disorder with dysmorphic facies and variable seizures (MONDO:0031011)

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
entinostat	increases expression, affects cotreatment	2
Benzo(a)pyrene	affects methylation, decreases expression	2
Estradiol	affects cotreatment, decreases expression	2
Valproic Acid	affects expression, increases expression	2
mono-(2-ethylhexyl)phthalate	decreases expression	1
perfluorooctanoic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Sunitinib	increases expression	1
Atrazine	increases expression	1
Carbamazepine	affects expression	1
Lead	affects expression	1
Phthalic Acids	increases methylation	1
Silicon Dioxide	decreases expression	1
Aflatoxin B1	decreases expression	1

Clinical trials (associated diseases)

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