GARIN1A

Summary

GARIN1A (golgi associated RAB2 interactor 1A, HGNC:27998) is a protein-coding gene on chromosome 7q32.1, encoding Golgi-associated RAB2 interactor protein 1A (Q6NXP2). RAB2B effector protein required for accurate acrosome formation and normal male fertility.

Predicted to be involved in acrosome assembly. Predicted to be located in Golgi apparatus.

Source: NCBI Gene 346653 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 61 total
• MANE Select transcript: NM_001128926

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27998
Approved symbol	GARIN1A
Name	golgi associated RAB2 interactor 1A
Location	7q32.1
Locus type	gene with protein product
Status	Approved
Aliases	GARI
Ensembl gene	ENSG00000205085
Ensembl biotype	protein_coding
OMIM	619904
Entrez	346653

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 6 nonsense_mediated_decay, 4 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000477515, ENST00000641143, ENST00000641443, ENST00000641605, ENST00000641888, ENST00000641987, ENST00000682356, ENST00000682361, ENST00000683523, ENST00000684390, ENST00000684498, ENST00000684742

RefSeq mRNA: 4 — MANE Select: NM_001128926 NM_001012454, NM_001128926, NM_001290254, NM_001290255

CCDS: CCDS47701, CCDS47702

Canonical transcript exons

ENST00000682356 — 5 exons

Exon	Start	End
ENSE00003537090	128675675	128675859
ENSE00003804479	128677564	128677813
ENSE00003809588	128680031	128680149
ENSE00003813076	128672292	128672550
ENSE00003919648	128682964	128687877

Expression profiles

Bgee: expression breadth ubiquitous, 163 present calls, max score 94.62.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0237 / max 16.6901, expressed in 4 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
204684	0.0120	3
80929	0.0117	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	94.62	gold quality
right testis	UBERON:0004534	88.85	gold quality
left testis	UBERON:0004533	87.99	gold quality
testis	UBERON:0000473	84.84	gold quality
buccal mucosa cell	CL:0002336	79.25	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.48	gold quality
apex of heart	UBERON:0002098	76.70	gold quality
right adrenal gland cortex	UBERON:0035827	73.62	gold quality
hindlimb stylopod muscle	UBERON:0004252	73.57	gold quality
adult organism	UBERON:0007023	72.69	gold quality
right adrenal gland	UBERON:0001233	72.46	gold quality
adenohypophysis	UBERON:0002196	72.10	gold quality
heart left ventricle	UBERON:0002084	71.52	gold quality
gastrocnemius	UBERON:0001388	71.32	gold quality
left adrenal gland	UBERON:0001234	71.10	gold quality
muscle of leg	UBERON:0001383	70.81	gold quality
left adrenal gland cortex	UBERON:0035825	70.69	gold quality
cardiac ventricle	UBERON:0002082	70.52	gold quality
right atrium auricular region	UBERON:0006631	70.41	gold quality
bone marrow cell	CL:0002092	70.31	silver quality
pituitary gland	UBERON:0000007	70.22	gold quality
stromal cell of endometrium	CL:0002255	69.84	gold quality
minor salivary gland	UBERON:0001830	69.31	gold quality
metanephros cortex	UBERON:0010533	69.18	gold quality
right coronary artery	UBERON:0001625	69.16	gold quality
adrenal cortex	UBERON:0001235	69.14	gold quality
right hemisphere of cerebellum	UBERON:0014890	69.14	gold quality
mucosa of stomach	UBERON:0001199	69.04	gold quality
cardiac atrium	UBERON:0002081	69.04	gold quality
right frontal lobe	UBERON:0002810	68.79	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.89
E-CURD-135	no	627.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

146 targeting GARIN1A, 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-6851-5P	100.00	65.63	1294
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-515-5P	99.92	69.82	2343

Literature-anchored findings (GeneRIF, showing 1)

• validated occurrence of an unusual TG 3’ splice site in intron 1 (PMID:17672918)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Garin1a	ENSMUSG00000079652
rattus_norvegicus	Garin1a	ENSRNOG00000039383

Paralogs (7): GARIN1B (ENSG00000135248), GARIN5A (ENSG00000142530), GARIN4 (ENSG00000162771), GARIN3 (ENSG00000170613), GARIN2 (ENSG00000172717), GARIN5B (ENSG00000180043), GARIN6 (ENSG00000180219)

Protein

Protein identifiers

Golgi-associated RAB2 interactor protein 1A — Q6NXP2 (reviewed: Q6NXP2)

All UniProt accessions (7): Q6NXP2, A0A804HIQ6, A0A804HJ82, A0A804HJA3, A0A804HKS5, A0A804HLI1, C9K0C0

UniProt curated annotations — full annotation on UniProt →

Function. RAB2B effector protein required for accurate acrosome formation and normal male fertility.

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?
Q6NXP2-1	1	yes
Q6NXP2-2	2

RefSeq proteins (4): NP_001012457, NP_001122398, NP_001277183, NP_001277184 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR022168	GARIL-like_Rab2B-bd	Domain

Pfam: PF12480

UniProt features (9 total): sequence variant 4, modified residue 3, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6NXP2-F1	64.48	0.31

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 (3): 231, 263, 267

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 40 (showing top): GOBP_VESICLE_ORGANIZATION, GOBP_MALE_GAMETE_GENERATION, GOBP_SECRETORY_GRANULE_ORGANIZATION, GOBP_CELLULAR_COMPONENT_ASSEMBLY_INVOLVED_IN_MORPHOGENESIS, chr7q32, GOBP_ACROSOME_ASSEMBLY, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP, MARTENS_TRETINOIN_RESPONSE_UP, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_DN, MIR4729, MIR506_3P

GO Biological Process (1): acrosome assembly (GO:0001675)

GO Molecular Function (1): protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
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
binding	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

206 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GARIN1A	OR51A4	Q8NGJ6	575
GARIN1A	TOGARAM2	Q6ZUX3	471
GARIN1A	DRD1	P21728	446
GARIN1A	PLEKHS1	Q5SXH7	396
GARIN1A	CCDC181	Q5TID7	395
GARIN1A	AGTPBP1	Q9UPW5	348
GARIN1A	POLN	Q7Z5Q5	348
GARIN1A	ANKRD55	Q3KP44	325
GARIN1A	CYP4F12	Q9HCS2	325
GARIN1A	RNF169	Q8NCN4	324
GARIN1A	ADAMTSL5	Q6ZMM2	323
GARIN1A	STXBP3	O00186	323
GARIN1A	HAPLN3	Q96S86	321
GARIN1A	GABRQ	Q9UN88	315
GARIN1A	SPIN2A	Q99865	280

IntAct

3 interactions, top by confidence:

A	B	Type	Score
GARIN1A	RAB2A	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): RAB2B (Affinity Capture-MS), RAB2A (Affinity Capture-MS), FAM71F2 (Two-hybrid), FAM71F2 (Two-hybrid), RAB2B (Affinity Capture-MS), RAB2A (Affinity Capture-MS), SERAC1 (Affinity Capture-MS), TMEM263 (Affinity Capture-MS)

ESM2 similar proteins: A2CI98, A6NMN3, A7MBB4, B2RXB0, B4F6Q9, D3YV92, F1M5M3, F1MJR8, O43283, P15304, P56645, Q14CH0, Q1HKZ5, Q28F43, Q2KIP3, Q2NKQ1, Q2PFD7, Q2YDH8, Q3UPF5, Q3UZD7, Q3V1D5, Q4G017, Q4R767, Q5R7R7, Q5R8X7, Q5RA75, Q5RJN7, Q5SW75, Q61194, Q68FV5, Q6NRK3, Q6NXP2, Q6P995, Q75NT5, Q76I76, Q7M6U3, Q80TM9, Q8BPQ7, Q8BQU7, Q8CCC3

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	52
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

828 predictions. Top by Δscore:

Variant	Effect	Δscore
7:128677814:G:GG	donor_gain	1.0000
7:128672526:G:GA	donor_gain	0.9900
7:128675646:T:A	acceptor_gain	0.9900
7:128675653:T:G	acceptor_gain	0.9900
7:128677812:CA:C	donor_gain	0.9900
7:128683138:A:T	donor_gain	0.9900
7:128677698:G:A	acceptor_gain	0.9800
7:128677811:ACA:A	donor_gain	0.9800
7:128683096:GAA:G	donor_gain	0.9800
7:128672525:T:TA	donor_gain	0.9700
7:128677809:CAACA:C	donor_gain	0.9700
7:128677810:AACA:A	donor_gain	0.9700
7:128682933:A:AG	acceptor_gain	0.9700
7:128672398:A:AG	donor_gain	0.9600
7:128677562:A:AG	acceptor_gain	0.9600
7:128677563:G:GG	acceptor_gain	0.9600
7:128677697:T:TA	acceptor_gain	0.9600
7:128677847:A:AG	donor_gain	0.9600
7:128680126:A:T	donor_gain	0.9600
7:128683129:T:G	donor_gain	0.9600
7:128672546:TCCAG:T	donor_loss	0.9500
7:128672547:CCAG:C	donor_loss	0.9500
7:128672548:CAGGT:C	donor_loss	0.9500
7:128672549:AG:A	donor_loss	0.9500
7:128672550:GGTAC:G	donor_loss	0.9500
7:128672552:T:A	donor_loss	0.9500
7:128677559:TCCA:T	acceptor_loss	0.9500
7:128677561:CA:C	acceptor_loss	0.9500
7:128677575:T:TA	acceptor_gain	0.9500
7:128677811:ACAGT:A	donor_loss	0.9500

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000064770 (7:128700886 A>G), RS1000072266 (7:128681411 GTTTC>G,GTTTCTTTC), RS1000241607 (7:128694053 C>T), RS1000255953 (7:128687976 T>C,G), RS1000263853 (7:128700425 C>T), RS1000274623 (7:128706925 G>C), RS1000478832 (7:128681983 G>A), RS1000589935 (7:128689070 C>G,T), RS1000772045 (7:128682911 T>C), RS1000872947 (7:128682503 C>T), RS1000902707 (7:128689135 T>C), RS1000976688 (7:128677371 G>A,T), RS1000981042 (7:128695596 G>A), RS1001026233 (7:128682733 T>C), RS1001278921 (7:128678363 A>T)

Disease associations

OMIM: gene MIM:619904 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

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

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
sodium arsenite	decreases expression	1
theaflavin-3,3’-digallate	affects expression	1
Benzo(a)pyrene	increases methylation	1
Niclosamide	increases expression	1
Aflatoxin B1	decreases expression	1
Particulate Matter	decreases expression	1

Clinical trials (associated diseases)

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