GARIN1B

Summary

GARIN1B (golgi associated RAB2 interactor 1B, HGNC:30704) is a protein-coding gene on chromosome 7q32.1, encoding Golgi-associated RAB2 interactor protein 1B (Q96KD3). RAB2B effector protein required for accurate acrosome formation and normal male fertility.

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

Source: NCBI Gene 84691 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 46 total
• MANE Select transcript: NM_001282788

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30704
Approved symbol	GARIN1B
Name	golgi associated RAB2 interactor 1B
Location	7q32.1
Locus type	gene with protein product
Status	Approved
Aliases	NYD-SP18, GARI-L1
Ensembl gene	ENSG00000135248
Ensembl biotype	protein_coding
OMIM	619905
Entrez	84691

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 4 protein_coding, 2 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000315184, ENST00000466842, ENST00000469348, ENST00000471558, ENST00000483459, ENST00000484425, ENST00000485070, ENST00000493738, ENST00000621392

RefSeq mRNA: 3 — MANE Select: NM_001282788 NM_001282788, NM_001282789, NM_032599

CCDS: CCDS5804, CCDS64763, CCDS94192

Canonical transcript exons

ENST00000621392 — 7 exons

Exon	Start	End
ENSE00003435830	128731100	128731743
ENSE00003559423	128718831	128719083
ENSE00003564613	128729902	128730069
ENSE00003579371	128723197	128723318
ENSE00003586541	128726834	128726871
ENSE00003709471	128716813	128716997
ENSE00003933120	128715391	128715690

Expression profiles

Bgee: expression breadth ubiquitous, 121 present calls, max score 98.31.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.9441 / max 185.4348, expressed in 104 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
80930	0.7086	95
80932	0.1669	50
80933	0.0539	3
80931	0.0124	7
204685	0.0022	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	98.31	gold quality
left testis	UBERON:0004533	96.73	gold quality
right testis	UBERON:0004534	96.49	gold quality
testis	UBERON:0000473	93.52	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.13	gold quality
buccal mucosa cell	CL:0002336	79.26	silver quality
adult organism	UBERON:0007023	77.99	gold quality
tibialis anterior	UBERON:0001385	71.68	silver quality
epithelial cell of pancreas	CL:0000083	70.06	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	68.75	gold quality
ileal mucosa	UBERON:0000331	68.49	silver quality
pancreatic ductal cell	CL:0002079	68.40	silver quality
deltoid	UBERON:0001476	64.97	gold quality
upper arm skin	UBERON:0004263	64.53	gold quality
superficial temporal artery	UBERON:0001614	60.23	gold quality
tendon of biceps brachii	UBERON:0008188	59.56	gold quality
substantia nigra pars compacta	UBERON:0001965	58.74	silver quality
quadriceps femoris	UBERON:0001377	58.49	gold quality
parotid gland	UBERON:0001831	56.73	gold quality
vastus lateralis	UBERON:0001379	56.50	gold quality
medial globus pallidus	UBERON:0002477	56.20	gold quality
globus pallidus	UBERON:0001875	55.84	gold quality
nucleus accumbens	UBERON:0001882	55.42	gold quality
body of tongue	UBERON:0011876	55.24	gold quality
lateral globus pallidus	UBERON:0002476	54.84	gold quality
substantia nigra	UBERON:0002038	54.76	gold quality
midbrain	UBERON:0001891	54.66	gold quality
ventral tegmental area	UBERON:0002691	54.50	gold quality
pharyngeal mucosa	UBERON:0000355	54.40	gold quality
vena cava	UBERON:0004087	54.36	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	30.83
E-ANND-3	yes	4.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting GARIN1B, 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-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-548AU-3P	99.70	68.22	1373
HSA-MIR-451B	99.55	68.28	1380
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-135A-5P	99.36	71.85	1601
HSA-MIR-135B-5P	99.36	71.63	1613
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-153-3P	98.96	72.51	1644
HSA-MIR-6895-3P	98.79	65.69	996
HSA-MIR-198	98.70	67.32	920
HSA-MIR-5088-3P	98.29	66.63	1310
HSA-MIR-6867-3P	98.12	66.07	1305
HSA-MIR-4303	98.01	68.13	2304
HSA-MIR-5681A	97.99	67.17	1658
HSA-MIR-127-5P	97.78	67.64	869
HSA-MIR-1306-5P	97.11	64.04	755

Literature-anchored findings (GeneRIF, showing 5)

• The effect of the NYD-SP18 SNP on obesity was larger than the effect of FTO in FHS. The NYD-SP18 gene is described as testes development related, but little is known about the gene’s function or the mechanism by which it may influence risk for obesity. (PMID:18317470)
• Genetic variants within NYD-SP18 genes revealed a significant additive effect on BMI values in males. (PMID:26680676)
• Overweight/obese female carriers of the NYD-SP18 rs6971091 GG genotype exhibited a more beneficial response to the intensive lifestyle intervention than others. (PMID:26849538)
• genetic association studies in populations in Eastern Europe (Czech Republic, Lithuania, Poland, and Russia): Data suggest that an SNP in NYD-SP18 (rs6971091) is not associated with overweight/obesity in the adult populations studied (aged 45-75). (PMID:27237450)
• Decreased body weight in overweight/obese children is not significantly influenced by the NYD-SP18 rs6971091 or TMEM18 rs4854344 polymorphisms. Gene Indexing Project Expand All Collapse All Decreased body weight in overweight/obese children is not significantly influenced by the NYD-SP18 rs6971091 or TMEM18 rs4854344 polymorphisms. (PMID:30341978)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Garin1b	ENSMUSG00000039742
rattus_norvegicus	Garin1b	ENSRNOG00000006132

Paralogs (7): GARIN5A (ENSG00000142530), GARIN4 (ENSG00000162771), GARIN3 (ENSG00000170613), GARIN2 (ENSG00000172717), GARIN5B (ENSG00000180043), GARIN6 (ENSG00000180219), GARIN1A (ENSG00000205085)

Protein

Protein identifiers

Golgi-associated RAB2 interactor protein 1B — Q96KD3 (reviewed: Q96KD3)

Alternative names: Testis development protein NYD-SP18

All UniProt accessions (5): A0A140VJJ3, Q96KD3, F8WC62, F8WC78, H7C4R1

UniProt curated annotations — full annotation on UniProt →

Function. RAB2B effector protein required for accurate acrosome formation and normal male fertility. In complex with RAB2A/RAB2B, seems to suppress excessive vesicle trafficking during acrosome formation.

Subcellular location. Golgi apparatus.

Similarity. Belongs to the GARIN family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q96KD3-1	1	yes
Q96KD3-2	2
Q96KD3-3	3

RefSeq proteins (3): NP_001269717, NP_001269718, NP_115988 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR022168	GARIL-like_Rab2B-bd	Domain

Pfam: PF12480

UniProt features (7 total): splice variant 3, sequence variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96KD3-F1	62.45	0.23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 71 (showing top): GOBP_SINGLE_FERTILIZATION, GOBP_VESICLE_ORGANIZATION, GCANCTGNY_MYOD_Q6, GOBP_MALE_GAMETE_GENERATION, PAX8_B, NKX62_Q2, GOBP_SECRETORY_GRANULE_ORGANIZATION, GOBP_CELLULAR_COMPONENT_ASSEMBLY_INVOLVED_IN_MORPHOGENESIS, NF1_Q6_01, chr7q32, WTGAAAT_UNKNOWN, TCF11_01, GOBP_ACROSOME_ASSEMBLY, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM

GO Biological Process (2): acrosome assembly (GO:0001675), acrosome reaction (GO:0007340)

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
membrane fusion involved in acrosome reaction	1
single fertilization	1
reproductive process	1
acrosomal vesicle exocytosis	1
binding	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

544 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GARIN1B	TMEM225	Q6GV28	626
GARIN1B	SPACA4	Q8TDM5	623
GARIN1B	SPATA3	Q8NHX4	602
GARIN1B	TMEM270	Q6UE05	571
GARIN1B	C22orf23	Q9BZE7	571
GARIN1B	CIMIP4	O43247	570
GARIN1B	UBQLN3	Q9H347	549
GARIN1B	FSCN3	Q9NQT6	524
GARIN1B	CCDC54	Q8NEL0	515
GARIN1B	TMCO5A	Q8N6Q1	509
GARIN1B	GTSF1L	Q9H1H1	505
GARIN1B	TMCO2	Q7Z6W1	481
GARIN1B	CCDC187	A0A096LP49	480
GARIN1B	CAPN11	Q9UMQ6	479
GARIN1B	SPATS1	Q496A3	477

IntAct

2 interactions, top by confidence:

A	B	Type	Score
GARIN1B	STYX	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (6): FAM71F1 (Affinity Capture-MS), FAM71F1 (Two-hybrid), FAM71F1 (Positive Genetic), STYX (Affinity Capture-MS), FAM71F1 (Affinity Capture-MS), HTT (Affinity Capture-Luminescence)

ESM2 similar proteins: A0JNF3, A3KMW7, A6NFA0, B2RQL2, B2RV46, D3Z8E6, D3ZAP3, D3ZJ47, E9Q309, E9Q793, F5H4B4, O14513, O60303, Q0P5X5, Q1RMQ5, Q2KIP3, Q2KJG1, Q2T9M9, Q32LN6, Q3URK1, Q3V0J4, Q3V0M2, Q53FD0, Q5PQL8, Q5T5Y3, Q642A3, Q68FV5, Q6AYJ3, Q6AYP4, Q6ZVD7, Q7PCK7, Q8BJS7, Q8CB14, Q8CCC3, Q8CCG1, Q8CDL9, Q8K3V1, Q8K3V7, Q8N4H0, Q95LL2

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	34
Likely benign	4
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1182 predictions. Top by Δscore:

Variant	Effect	Δscore
7:128723196:GTTA:G	acceptor_gain	1.0000
7:128726794:A:AG	acceptor_gain	1.0000
7:128726795:A:G	acceptor_gain	1.0000
7:128726801:A:AG	acceptor_gain	1.0000
7:128718964:T:TA	acceptor_gain	0.9900
7:128723195:A:AG	acceptor_gain	0.9900
7:128723196:G:GA	acceptor_gain	0.9900
7:128723196:GTT:G	acceptor_gain	0.9900
7:128723314:T:G	donor_gain	0.9900
7:128726788:A:AG	acceptor_gain	0.9900
7:128726802:T:G	acceptor_gain	0.9900
7:128726808:T:A	acceptor_gain	0.9900
7:128729625:T:A	acceptor_gain	0.9900
7:128715686:TCCAG:T	donor_loss	0.9800
7:128715687:CCAGG:C	donor_loss	0.9800
7:128715688:CAG:C	donor_loss	0.9800
7:128715689:AGG:A	donor_loss	0.9800
7:128715690:GGTAT:G	donor_loss	0.9800
7:128718965:G:A	acceptor_gain	0.9800
7:128726789:C:G	acceptor_gain	0.9800
7:128726796:C:G	acceptor_gain	0.9800
7:128729623:ACT:A	acceptor_gain	0.9800
7:128729983:A:T	donor_gain	0.9800
7:128731092:A:AG	acceptor_gain	0.9800
7:128715627:G:GA	donor_gain	0.9700
7:128715691:G:GC	donor_loss	0.9700
7:128715692:T:A	donor_loss	0.9700
7:128716995:GAG:G	donor_gain	0.9700
7:128718890:A:AG	acceptor_gain	0.9700
7:128718891:G:GG	acceptor_gain	0.9700

AlphaMissense

2384 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:128715676:A:C	S79R	0.991
7:128715678:C:A	S79R	0.991
7:128715678:C:G	S79R	0.991
7:128718955:T:C	F187L	0.990
7:128718957:C:A	F187L	0.990
7:128718957:C:G	F187L	0.990
7:128718964:T:A	W190R	0.990
7:128718964:T:C	W190R	0.990
7:128715682:T:C	F81L	0.989
7:128715684:C:A	F81L	0.989
7:128715684:C:G	F81L	0.989
7:128715683:T:C	F81S	0.986
7:128716908:C:A	N115K	0.977
7:128716908:C:G	N115K	0.977
7:128718966:G:C	W190C	0.976
7:128718966:G:T	W190C	0.976
7:128716904:C:A	P114H	0.975
7:128718923:T:C	L176P	0.975
7:128715670:T:C	F77L	0.971
7:128715672:T:A	F77L	0.971
7:128715672:T:G	F77L	0.971
7:128715671:T:C	F77S	0.970
7:128718893:T:C	L166S	0.970
7:128718887:T:C	L164P	0.969
7:128715643:T:C	F68L	0.968
7:128715645:C:A	F68L	0.968
7:128715645:C:G	F68L	0.968
7:128715677:G:T	S79I	0.968
7:128716913:T:C	L117P	0.968
7:128718956:T:C	F187S	0.967

dbSNP variants (sampled 300 via entrez): RS1000021805 (7:128724924 C>A), RS1000307300 (7:128731583 A>C), RS1000450517 (7:128724963 T>C), RS1000495811 (7:128718424 C>G,T), RS1000588943 (7:128713329 C>G), RS1000720136 (7:128713645 A>T), RS1000795136 (7:128726748 G>A,C), RS1000846529 (7:128727119 C>T), RS1000937144 (7:128719387 A>G), RS1001000289 (7:128713242 G>A), RS1001176123 (7:128728411 C>T), RS1001326142 (7:128721766 T>C), RS1001338669 (7:128714655 G>T), RS1001339939 (7:128726210 G>A), RS1001389575 (7:128719796 C>T)

Disease associations

OMIM: gene MIM:619905 | 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

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases expression	7
trichostatin A	affects cotreatment, decreases expression	3
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
aristolochic acid I	increases expression	1
propionaldehyde	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
tetrabromobisphenol A	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Decitabine	affects expression	1
Panobinostat	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Carbamazepine	affects expression	1
Cisplatin	affects expression	1
Demecolcine	increases expression	1
Diethylhexyl Phthalate	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	decreases expression	1
Testosterone	decreases expression	1
Vincristine	increases expression	1

Clinical trials (associated diseases)

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