GARIN5B

Summary

GARIN5B (golgi associated RAB2 interactor family member 5B, HGNC:25278) is a protein-coding gene on chromosome 19q13.42, encoding Golgi-associated RAB2 interactor protein 5B (Q8N5Q1).

Predicted to act upstream of or within several processes, including flagellated sperm motility; penetration of zona pellucida; and spermatid development. Predicted to be active in sperm head.

Source: NCBI Gene 284418 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 218 total
• MANE Select transcript: NM_001145402

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25278
Approved symbol	GARIN5B
Name	golgi associated RAB2 interactor family member 5B
Location	19q13.42
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp434G1729
Ensembl gene	ENSG00000180043
Ensembl biotype	protein_coding
OMIM	621103
Entrez	284418

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 nonsense_mediated_decay

ENST00000424985, ENST00000585734

RefSeq mRNA: 1 — MANE Select: NM_001145402 NM_001145402

Canonical transcript exons

ENST00000424985 — 11 exons

Exon	Start	End
ENSE00001248696	55362917	55363260
ENSE00001409899	55361410	55361434
ENSE00001620531	55354908	55355095
ENSE00001730844	55360693	55360769
ENSE00001794243	55360853	55360905
ENSE00003501400	55358145	55359979
ENSE00003521233	55361174	55361238
ENSE00003539205	55362245	55362503
ENSE00003569447	55355260	55355345
ENSE00003655207	55362578	55362732
ENSE00003672106	55361000	55361103

Expression profiles

Bgee: expression breadth broad, 17 present calls, max score 87.10.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0812 / max 70.3693, expressed in 4 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182795	0.0812	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	87.10	gold quality
left testis	UBERON:0004533	86.89	gold quality
testis	UBERON:0000473	86.21	gold quality
bone marrow cell	CL:0002092	47.70	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	41.54	gold quality
colonic epithelium	UBERON:0000397	41.22	gold quality
stromal cell of endometrium	CL:0002255	40.56	silver quality
bone marrow	UBERON:0002371	37.64	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
right coronary artery	UBERON:0001625	35.64	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
left uterine tube	UBERON:0001303	35.40	gold quality
sural nerve	UBERON:0015488	35.03	gold quality
apex of heart	UBERON:0002098	34.83	gold quality
placenta	UBERON:0001987	34.31	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
liver	UBERON:0002107	31.46	gold quality
tonsil	UBERON:0002372	31.38	gold quality
cortex of kidney	UBERON:0001225	31.16	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
prefrontal cortex	UBERON:0000451	30.45	gold quality
fallopian tube	UBERON:0003889	30.42	silver quality
hypothalamus	UBERON:0001898	30.33	gold quality
metanephros cortex	UBERON:0010533	30.31	gold quality
monocyte	CL:0000576	29.72	gold quality
leukocyte	CL:0000738	29.53	gold quality
right uterine tube	UBERON:0001302	29.36	gold quality
duodenum	UBERON:0002114	28.14	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.66

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting GARIN5B, 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-548AN	99.97	70.91	2817
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-484	98.16	66.92	1074
HSA-MIR-3155A	98.16	66.09	965
HSA-MIR-3155B	98.16	66.09	965
HSA-MIR-4638-3P	97.90	65.75	905
HSA-MIR-148B-5P	97.29	66.30	992
HSA-MIR-6874-3P	97.29	66.34	975
HSA-MIR-4774-5P	95.92	68.27	827
HSA-MIR-7108-3P	94.37	64.79	183

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Garin5b	ENSMUSG00000092518
rattus_norvegicus	Garin5b	ENSRNOG00000033173

Paralogs (7): GARIN1B (ENSG00000135248), GARIN5A (ENSG00000142530), GARIN4 (ENSG00000162771), GARIN3 (ENSG00000170613), GARIN2 (ENSG00000172717), GARIN6 (ENSG00000180219), GARIN1A (ENSG00000205085)

Protein

Protein identifiers

Golgi-associated RAB2 interactor protein 5B — Q8N5Q1 (reviewed: Q8N5Q1)

All UniProt accessions (2): Q8N5Q1, K7EMA1

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the GARIN family.

RefSeq proteins (1): NP_001138874* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR022168	GARIL-like_Rab2B-bd	Domain

Pfam: PF12480

UniProt features (18 total): region of interest 6, compositionally biased region 6, sequence conflict 4, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N5Q1-F1	44.12	0.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 10 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, MARTENS_TRETINOIN_RESPONSE_UP, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_UP, HMGB2_TARGET_GENES, GSE12839_CTRL_VS_IL12_TREATED_PBMC_UP, GSE37416_CTRL_VS_0H_F_TULARENSIS_LVS_NEUTROPHIL_UP, chr19q13, GSE6259_33D1_POS_DC_VS_CD8_TCELL_UP, GSE41867_DAY6_VS_DAY15_LCMV_ARMSTRONG_EFFECTOR_CD8_TCELL_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

1486 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GARIN5B	C1orf210	Q8IVY1	583
GARIN5B	OR9G1	Q8NH87	571
GARIN5B	C14orf132	Q9NPU4	506
GARIN5B	RGSL1	A5PLK6	487
GARIN5B	TTLL2	Q9BWV7	479
GARIN5B	HEPACAM2	A8MVW5	404
GARIN5B	ZBED8L	Q8TCP9	394
GARIN5B	BOD1L2	Q8IYS8	376
GARIN5B	ZPBP2	Q6X784	365
GARIN5B	ZBED11	P0CF97	360
GARIN5B	PCYT2	Q99447	357
GARIN5B	F5GXT2	F5GXT2	355
GARIN5B	DYNLRB2	Q8TF09	350
GARIN5B	DNAAF1	Q8NEP3	339
GARIN5B	CCT8L2	Q96SF2	326

IntAct

4 interactions, top by confidence:

A	B	Type	Score
GARIN5B	HIST2H2BF	psi-mi:“MI:0915”(physical association)	0.400
GARIN5B	USP11	psi-mi:“MI:0915”(physical association)	0.400
ALB	SH3BP5	psi-mi:“MI:0914”(association)	0.350

BioGRID (12): FAM71E2 (Two-hybrid), KRTAP10-3 (Two-hybrid), NOTCH2NL (Two-hybrid), FAM71E2 (Two-hybrid), FAM71E2 (Proximity Label-MS), FAM71E2 (Protein-peptide), FAM71E2 (Cross-Linking-MS (XL-MS)), RPL4 (Cross-Linking-MS (XL-MS)), RPL6 (Cross-Linking-MS (XL-MS)), HIST1H3A (Cross-Linking-MS (XL-MS)), FAM71E2 (Cross-Linking-MS (XL-MS)), FAM71E2 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTH6, A0A1B0GUW6, A0A1D5RMD1, A2AQH4, A4FU49, A6NJ88, C4P6S0, D3YU32, E9PAV3, F1QU13, I3L273, J3KML8, P70670, Q32L62, Q3V0E1, Q3V3Q4, Q4R729, Q5H9F3, Q5QJ38, Q5SWP3, Q5U4C1, Q5VWK0, Q5VYM1, Q68DN1, Q6AZ54, Q7TSG5, Q810T2, Q8CH19, Q8K4E0, Q8N3K9, Q8N5Q1, Q8NDH2, Q8TCU4, Q8WNU4, Q8WWL7, Q920R4, Q921B4, Q923B3, Q96JA4, Q96M34

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	192
Likely benign	22
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1565 predictions. Top by Δscore:

Variant	Effect	Δscore
19:55358175:T:TA	donor_gain	1.0000
19:55360995:C:CA	donor_gain	1.0000
19:55360998:A:AC	donor_gain	1.0000
19:55360999:C:CC	donor_gain	1.0000
19:55360999:CTT:C	donor_gain	1.0000
19:55361001:T:TA	donor_gain	1.0000
19:55361019:T:TA	donor_gain	1.0000
19:55361182:T:A	donor_gain	1.0000
19:55361235:CTGA:C	acceptor_gain	1.0000
19:55361236:TGA:T	acceptor_gain	1.0000
19:55361239:C:CC	acceptor_gain	1.0000
19:55355063:T:TA	donor_gain	0.9900
19:55355255:GGTAC:G	donor_loss	0.9900
19:55355256:GTAC:G	donor_loss	0.9900
19:55355257:TAC:T	donor_loss	0.9900
19:55355258:A:C	donor_loss	0.9900
19:55355259:C:CA	donor_loss	0.9900
19:55355342:CAGG:C	acceptor_gain	0.9900
19:55355343:AGG:A	acceptor_gain	0.9900
19:55355345:GC:G	acceptor_loss	0.9900
19:55355346:C:CC	acceptor_gain	0.9900
19:55355347:T:G	acceptor_loss	0.9900
19:55358172:T:TA	donor_gain	0.9900
19:55359975:CAGGC:C	acceptor_gain	0.9900
19:55359976:AGGC:A	acceptor_gain	0.9900
19:55359977:GGC:G	acceptor_gain	0.9900
19:55359978:GC:G	acceptor_gain	0.9900
19:55359978:GCCTG:G	acceptor_loss	0.9900
19:55359979:CC:C	acceptor_gain	0.9900
19:55359979:CCTG:C	acceptor_loss	0.9900

AlphaMissense

5901 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:55362923:A:C	F48L	0.981
19:55362923:A:T	F48L	0.981
19:55362925:A:G	F48L	0.981
19:55362929:A:C	S46R	0.973
19:55362929:A:T	S46R	0.973
19:55362931:T:G	S46R	0.973
19:55362371:G:C	F146L	0.972
19:55362371:G:T	F146L	0.972
19:55362373:A:G	F146L	0.972
19:55362924:A:G	F48S	0.970
19:55362935:G:C	F44L	0.965
19:55362935:G:T	F44L	0.965
19:55362937:A:G	F44L	0.965
19:55362924:A:C	F48C	0.960
19:55362632:A:G	L84S	0.954
19:55362498:A:G	I104T	0.953
19:55362364:A:G	W149R	0.950
19:55362364:A:T	W149R	0.950
19:55362362:C:A	W149C	0.947
19:55362362:C:G	W149C	0.947
19:55362641:G:T	P81H	0.947
19:55362917:C:A	Q50H	0.943
19:55362917:C:G	Q50H	0.943
19:55362629:A:G	L85P	0.942
19:55362623:C:T	G87D	0.940
19:55362411:A:G	L133P	0.939
19:55362377:G:C	F144L	0.936
19:55362377:G:T	F144L	0.936
19:55362379:A:G	F144L	0.936
19:55362668:G:T	A72D	0.936

dbSNP variants (sampled 300 via entrez): RS1000123338 (19:55362968 G>A,T), RS1000536843 (19:55362291 AG>A,AGG), RS1000978796 (19:55356816 C>T), RS1000995902 (19:55357671 C>T), RS1001263555 (19:55358824 C>T), RS1001385968 (19:55364029 C>G), RS1001667459 (19:55364295 C>A,T), RS1001895217 (19:55363949 G>A), RS1002270410 (19:55363314 C>A,T), RS1002577253 (19:55358150 C>A), RS1002851114 (19:55360723 G>A), RS1002944674 (19:55361028 C>T), RS1002950252 (19:55359767 C>T), RS1002999048 (19:55355376 T>C), RS1003164805 (19:55365117 ATCACCTGAGG>A)

Disease associations

OMIM: gene MIM:621103 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST005025_11	Anti-saccade response	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006874	antisaccade response measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
butyraldehyde	increases expression	1
abrine	increases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Thiram	increases expression	1
Triclosan	increases expression	1
Valproic Acid	increases methylation	1
1-Methyl-4-phenylpyridinium	increases expression	1

Clinical trials (associated diseases)

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