GARIN6

Summary

GARIN6 (golgi associated RAB2 interactor family member 6, HGNC:28594) is a protein-coding gene on chromosome 12q23.1, encoding Golgi-associated RAB2 interactor protein 6 (Q8NEG0).

At a glance

• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_153364

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28594
Approved symbol	GARIN6
Name	golgi associated RAB2 interactor family member 6
Location	12q23.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC39520
Ensembl gene	ENSG00000180219
Ensembl biotype	protein_coding
Entrez	196472

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000324341

RefSeq mRNA: 1 — MANE Select: NM_153364 NM_153364

CCDS: CCDS9072

Canonical transcript exons

ENST00000324341 — 2 exons

Exon	Start	End
ENSE00001227163	99649288	99650114
ENSE00001291290	99647753	99648789

Expression profiles

Bgee: expression breadth broad, 16 present calls, max score 95.55.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0531 / max 41.5532, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
127558	0.0531	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	95.55	gold quality
right testis	UBERON:0004534	88.29	gold quality
left testis	UBERON:0004533	87.61	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.10	gold quality
testis	UBERON:0000473	84.74	gold quality
adult organism	UBERON:0007023	67.74	gold quality
endothelial cell	CL:0000115	59.75	gold quality
epithelium of nasopharynx	UBERON:0001951	57.04	gold quality
esophagus squamous epithelium	UBERON:0006920	55.94	gold quality
mammary duct	UBERON:0001765	53.95	gold quality
oocyte	CL:0000023	52.60	gold quality
cerebellar vermis	UBERON:0004720	52.56	gold quality
cardia of stomach	UBERON:0001162	50.42	gold quality
nasal cavity epithelium	UBERON:0005384	48.71	gold quality
Brodmann (1909) area 46	UBERON:0006483	48.01	gold quality
colonic epithelium	UBERON:0000397	47.29	gold quality
thymus	UBERON:0002370	46.73	gold quality
buccal mucosa cell	CL:0002336	45.83	gold quality
vastus lateralis	UBERON:0001379	44.35	gold quality
amniotic fluid	UBERON:0000173	44.27	gold quality
quadriceps femoris	UBERON:0001377	44.24	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
pharyngeal mucosa	UBERON:0000355	43.05	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
germinal epithelium of ovary	UBERON:0001304	42.30	gold quality
visceral pleura	UBERON:0002401	42.23	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

43 targeting GARIN6, 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-3134	100.00	66.43	777
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-10395-5P	99.86	67.35	676
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-6715B-5P	99.64	69.63	1420
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-4269	99.55	69.89	1373
HSA-MIR-12132	99.47	68.90	1341
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-5580-5P	99.38	66.96	1139
HSA-MIR-329-5P	99.27	68.11	1597
HSA-MIR-6878-3P	99.24	64.23	920
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-5590-5P	98.81	68.78	969
HSA-MIR-655-5P	98.74	65.93	888
HSA-MIR-1246	98.54	66.21	959
HSA-MIR-7156-3P	98.25	67.66	859
HSA-MIR-1233-5P	98.19	66.71	1201
HSA-MIR-6778-5P	98.19	66.59	1239

Cross-species orthologs

0 orthologs

Paralogs (7): GARIN1B (ENSG00000135248), GARIN5A (ENSG00000142530), GARIN4 (ENSG00000162771), GARIN3 (ENSG00000170613), GARIN2 (ENSG00000172717), GARIN5B (ENSG00000180043), GARIN1A (ENSG00000205085)

Protein

Protein identifiers

Golgi-associated RAB2 interactor protein 6 — Q8NEG0 (reviewed: Q8NEG0)

All UniProt accessions (1): Q8NEG0

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the GARIN family.

RefSeq proteins (1): NP_699195* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR022168	GARIL-like_Rab2B-bd	Domain

Pfam: PF12480

UniProt features (4 total): sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NEG0-F1	70.95	0.43

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 23 (showing top): WTGAAAT_UNKNOWN, GATA1_03, chr12q23, MARTENS_TRETINOIN_RESPONSE_UP, MIR1290, MIR3158_5P, MIR6715B_5P, MIR509_5P, MIR509_3_5P, MIR4776_3P, MIR6778_5P, MIR1233_5P, MIR2278, MIR4468, MIR10395_5P

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

170 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GARIN6	ZNF438	Q7Z4V0	480
GARIN6	SUSD1	Q6UWL2	479
GARIN6	ZNF8	P17098	467
GARIN6	CCDC91	Q7Z6B0	418
GARIN6	TAF1C	Q15572	379
GARIN6	TTC23L	Q6PF05	360
GARIN6	ANKS1B	Q7Z6G8	336
GARIN6	ADHFE1	Q8IWW8	336
GARIN6	PARD3B	Q8TEW8	327
GARIN6	KIF21B	O75037	318
GARIN6	BRK1	Q8WUW1	310
GARIN6	ZNF605	Q86T29	304
GARIN6	ZNF615	Q8N8J6	293
GARIN6	SCTR	P47872	277
GARIN6	PTP4A3	O75365	270
GARIN6	FGL1	Q08830	270

IntAct

192 interactions, top by confidence:

A	B	Type	Score
RAB2A	GARIN6	psi-mi:“MI:0915”(physical association)	0.780
GARIN6	RAB2A	psi-mi:“MI:0915”(physical association)	0.780
KRT31	GARIN6	psi-mi:“MI:0915”(physical association)	0.720
GARIN6	RAB2B	psi-mi:“MI:0915”(physical association)	0.720
RAB2B	GARIN6	psi-mi:“MI:0915”(physical association)	0.720
GARIN6	KRT31	psi-mi:“MI:0915”(physical association)	0.720
FHL3	GARIN6	psi-mi:“MI:0915”(physical association)	0.560
GARIN6	KRT40	psi-mi:“MI:0915”(physical association)	0.560
GARIN6	NOTCH2NLA	psi-mi:“MI:0915”(physical association)	0.560
GARIN6	BANP	psi-mi:“MI:0915”(physical association)	0.560
GARIN6	FHL3	psi-mi:“MI:0915”(physical association)	0.560
KRT40	GARIN6	psi-mi:“MI:0915”(physical association)	0.560
BANP	GARIN6	psi-mi:“MI:0915”(physical association)	0.560
NOTCH2NLA	GARIN6	psi-mi:“MI:0915”(physical association)	0.560
GARIN6	RAB14	psi-mi:“MI:0915”(physical association)	0.560
KRT34	GARIN6	psi-mi:“MI:0915”(physical association)	0.560
RAB4B	GARIN6	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (26): FAM71C (Two-hybrid), FAM71C (Two-hybrid), FAM71C (Two-hybrid), FAM71C (Two-hybrid), FAM71C (Two-hybrid), FAM71C (Two-hybrid), NOTCH2NL (Two-hybrid), FAM71C (Two-hybrid), FAM71C (Two-hybrid), FAM71C (Two-hybrid), FAM71C (Two-hybrid), FAM71C (Two-hybrid), FAM71C (Two-hybrid), FAM71C (Two-hybrid), FAM71C (Two-hybrid)

ESM2 similar proteins: A0A1L8HTT5, A4IIM9, A6NFN9, A9ZLX4, D3YYM4, F1MN90, M0R2J8, O15259, O54828, O60543, O70302, O70303, O75916, P49805, P56198, Q3B7M3, Q3T191, Q3U827, Q4R323, Q4R899, Q4VXA5, Q5JV73, Q5SUS0, Q5SYB0, Q5XI33, Q5XX13, Q61137, Q6AY22, Q6P9P8, Q6ZPF3, Q7TNY7, Q7TP54, Q7TP65, Q80U16, Q80VH0, Q8BLA1, Q8C0W1, Q8K3I4, Q8N2C3, Q8N9Z9

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.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 96 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
Ras activation upon Ca2+ influx through NMDA receptor	5	42.0×	5e-06
Unblocking of NMDA receptors, glutamate binding and activation	5	40.0×	5e-06
Negative regulation of NMDA receptor-mediated neuronal transmission	5	40.0×	5e-06
Long-term potentiation	5	35.0×	8e-06
Assembly and cell surface presentation of NMDA receptors	9	33.6×	5e-10
Neurexins and neuroligins	10	29.0×	3e-10
Protein-protein interactions at synapses	7	27.3×	4e-07
RAB geranylgeranylation	5	12.7×	8e-04

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	11	71.0×	8e-16
protein localization to synapse	6	51.1×	2e-07
receptor clustering	7	48.5×	2e-08
regulation of postsynaptic membrane neurotransmitter receptor levels	6	33.0×	2e-06
cell-cell adhesion	10	11.3×	2e-06
protein-containing complex assembly	8	10.1×	6e-05
Golgi organization	6	8.9×	1e-03
actin cytoskeleton organization	7	6.2×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

124 predictions. Top by Δscore:

Variant	Effect	Δscore
12:99648769:G:GT	donor_gain	0.9900
12:99648787:GTG:G	donor_gain	0.9900
12:99648790:GT:G	donor_loss	0.9900
12:99648791:T:G	donor_loss	0.9900
12:99648792:GA:G	donor_loss	0.9900
12:99648790:G:GG	donor_gain	0.9800
12:99648793:AG:A	donor_loss	0.9800
12:99649286:AG:A	acceptor_gain	0.9300
12:99649287:GG:G	acceptor_gain	0.9300
12:99649287:GGGAT:G	acceptor_gain	0.9300
12:99649282:CCCTA:C	acceptor_loss	0.9200
12:99649283:CCTA:C	acceptor_loss	0.9200
12:99649284:CTAG:C	acceptor_loss	0.9200
12:99649285:TAG:T	acceptor_loss	0.9200
12:99649287:G:A	acceptor_loss	0.9200
12:99648719:A:AG	donor_gain	0.9000
12:99649271:ATTT:A	acceptor_loss	0.8900
12:99649286:A:AG	acceptor_gain	0.8600
12:99649287:G:GG	acceptor_gain	0.8600
12:99648785:CAGTG:C	donor_gain	0.8500
12:99648788:TG:T	donor_gain	0.8500
12:99648789:GG:G	donor_gain	0.8500
12:99649274:T:TA	acceptor_loss	0.8500
12:99649286:AGG:A	acceptor_gain	0.8400
12:99649287:GGG:G	acceptor_gain	0.8400
12:99648769:G:T	donor_gain	0.8300
12:99649272:T:G	acceptor_loss	0.8300
12:99648786:AGTG:A	donor_gain	0.7700
12:99648787:GTGG:G	donor_gain	0.7700
12:99648788:TGGT:T	donor_gain	0.7700

AlphaMissense

1602 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:99648322:T:C	F50L	0.994
12:99648324:T:A	F50L	0.994
12:99648324:T:G	F50L	0.994
12:99648323:T:C	F50S	0.990
12:99648616:T:C	F148L	0.986
12:99648618:T:A	F148L	0.986
12:99648618:T:G	F148L	0.986
12:99648661:T:C	F163L	0.986
12:99648663:T:A	F163L	0.986
12:99648663:T:G	F163L	0.986
12:99648670:T:A	W166R	0.985
12:99648670:T:C	W166R	0.985
12:99648672:G:C	W166C	0.985
12:99648672:G:T	W166C	0.985
12:99648316:A:C	S48R	0.984
12:99648318:C:A	S48R	0.984
12:99648318:C:G	S48R	0.984
12:99648422:C:A	P83H	0.982
12:99648235:T:C	F21L	0.978
12:99648237:T:A	F21L	0.978
12:99648237:T:G	F21L	0.978
12:99648293:T:C	F40S	0.976
12:99648593:T:C	L140P	0.976
12:99648623:T:C	L150P	0.975
12:99648584:A:C	Q137P	0.974
12:99648395:T:A	V74D	0.973
12:99648421:C:T	P83S	0.973
12:99648434:T:A	L87Q	0.971
12:99648323:T:G	F50C	0.970
12:99648671:G:C	W166S	0.970

dbSNP variants (sampled 300 via entrez): RS1000161240 (12:99647144 C>T), RS1001030962 (12:99647208 T>C), RS1002042865 (12:99646227 A>G), RS1002279155 (12:99647897 G>C), RS1002289104 (12:99647715 T>A,C,G), RS1003616845 (12:99650500 CCA>C), RS1003965546 (12:99649151 A>G), RS1004396521 (12:99649743 G>A), RS1004786456 (12:99650076 AT>A), RS1005507308 (12:99649569 G>A), RS1005960365 (12:99648859 C>T), RS1005968545 (12:99648635 C>G,T), RS1006508574 (12:99648034 A>T), RS1006789488 (12:99647760 G>C), RS1007509746 (12:99646586 G>A)

Disease associations

OMIM: gene `` | 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

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

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Valproic Acid	increases methylation	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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