GOLGA6B

Summary

GOLGA6B (golgin A6 family member B, HGNC:32205) is a protein-coding gene on chromosome 15q24.1, encoding Golgin subfamily A member 6B (A6NDN3). It is a selective cancer dependency (DepMap: 32.8% of cell lines).

This gene is found in a large, low copy repeat sequence or duplicon that is found in multiple copies, which are greater than 90% similar, on chromosome 15. Duplicons are associated with deletions, inversions and other chromosomal rearrangements that underlie genomic disease. This gene is a member of the golgin gene family, whose protein products localize to the Golgi apparatus. The majority of the related gene copies are thought to be transcribed pseudogenes. It is not known whether this gene is a pseudogene or if it encodes a golgin protein.

Source: NCBI Gene 55889 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 112 total
• Cancer dependency (DepMap): dependent in 32.8% of screened cell lines
• MANE Select transcript: NM_018652

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32205
Approved symbol	GOLGA6B
Name	golgin A6 family member B
Location	15q24.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000215186
Ensembl biotype	protein_coding
Entrez	55889

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000421285, ENST00000568532, ENST00000909077

RefSeq mRNA: 1 — MANE Select: NM_018652 NM_018652

CCDS: CCDS10245

Canonical transcript exons

ENST00000421285 — 18 exons

Exon	Start	End
ENSE00001824832	72666215	72669599
ENSE00002435884	72659794	72659844
ENSE00002446790	72665782	72665885
ENSE00002450746	72656512	72656631
ENSE00002451973	72660123	72660229
ENSE00002458376	72664944	72665035
ENSE00002470328	72665975	72666128
ENSE00002485059	72661759	72661846
ENSE00002498053	72661459	72661566
ENSE00002498230	72661264	72661350
ENSE00002500604	72664436	72664511
ENSE00002508646	72659945	72660026
ENSE00002511800	72665596	72665698
ENSE00002512115	72663037	72663105
ENSE00002529871	72662252	72662760
ENSE00002586635	72654697	72654821
ENSE00003539261	72659494	72659532
ENSE00003605917	72658558	72658638

Expression profiles

Bgee: expression breadth broad, 92 present calls, max score 80.70.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.70	gold quality
right testis	UBERON:0004534	74.96	gold quality
left testis	UBERON:0004533	74.64	gold quality
testis	UBERON:0000473	74.24	gold quality
liver	UBERON:0002107	57.48	gold quality
right uterine tube	UBERON:0001302	54.35	gold quality
right lobe of liver	UBERON:0001114	50.82	gold quality
primary visual cortex	UBERON:0002436	48.35	gold quality
skeletal muscle tissue	UBERON:0001134	46.63	gold quality
muscle tissue	UBERON:0002385	41.95	gold quality
left uterine tube	UBERON:0001303	41.68	gold quality
ectocervix	UBERON:0012249	41.22	gold quality
apex of heart	UBERON:0002098	40.77	silver quality
right ovary	UBERON:0002118	40.51	gold quality
mucosa of stomach	UBERON:0001199	39.52	silver quality
lower esophagus mucosa	UBERON:0035834	38.62	gold quality
ovary	UBERON:0000992	38.05	silver quality
skin of leg	UBERON:0001511	37.89	gold quality
gastrocnemius	UBERON:0001388	37.64	gold quality
tibial artery	UBERON:0007610	37.59	gold quality
subcutaneous adipose tissue	UBERON:0002190	37.55	gold quality
zone of skin	UBERON:0000014	37.49	gold quality
popliteal artery	UBERON:0002250	37.41	gold quality
tibial nerve	UBERON:0001323	37.27	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
skin of abdomen	UBERON:0001416	37.00	gold quality
muscle of leg	UBERON:0001383	36.98	gold quality
uterine cervix	UBERON:0000002	36.70	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-CURD-10	no	40.44
E-ANND-3	no	0.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting GOLGA6B, 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-3646	100.00	73.56	5283
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-1179	99.71	68.70	1040
HSA-MIR-10393-5P	99.65	68.01	1368
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-2113	99.58	71.22	1521
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-4677-3P	99.49	67.91	1246
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-513A-3P	99.39	70.63	3620
HSA-MIR-513C-3P	99.39	70.63	3620
HSA-MIR-6128	99.33	67.83	1581
HSA-MIR-7158-5P	99.25	67.95	796
HSA-MIR-5693	99.24	66.67	1106

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 32.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• Golgi Apparatus Target Proteins in Gastroenterological Cancers: A Comprehensive Review of GOLPH3 and GOLGA Proteins. (PMID:37508488)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	golga2	ENSDARG00000063197
mus_musculus	Golga2	ENSMUSG00000002546
rattus_norvegicus	Golga2l1	ENSRNOG00000050262
drosophila_melanogaster	GM130	FBGN0034697
caenorhabditis_elegans		WBGENE00018017

Paralogs (18): GOLGA6D (ENSG00000140478), GOLGA8F (ENSG00000153684), GOLGA6A (ENSG00000159289), GOLGA2 (ENSG00000167110), GOLGA6C (ENSG00000167195), GOLGA8A (ENSG00000175265), GOLGA8Q (ENSG00000178115), GOLGA8J (ENSG00000179938), GOLGA8G (ENSG00000183629), GOLGA8R (ENSG00000186399), GOLGA8M (ENSG00000188626), GOLGA8O (ENSG00000206127), GOLGA8B (ENSG00000215252), GOLGA8N (ENSG00000232653), GOLGA8K (ENSG00000249931), GOLGA8T (ENSG00000261247), GOLGA8S (ENSG00000261739), GOLGA8H (ENSG00000261794)

Protein

Protein identifiers

Golgin subfamily A member 6B — A6NDN3 (reviewed: A6NDN3)

All UniProt accessions (1): A6NDN3

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the GOLGA6 family.

RefSeq proteins (1): NP_061122* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024858	GOLGA	Family
IPR043976	GOLGA_cons_dom	Domain

Pfam: PF15070

UniProt features (9 total): region of interest 4, compositionally biased region 2, chain 1, coiled-coil region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NDN3-F1	74.07	0.48

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_GOLGI_ORGANIZATION, GOCC_GOLGI_STACK, GOCC_GOLGI_CISTERNA, GOCC_CIS_GOLGI_NETWORK, GOCC_GOLGI_CISTERNA_MEMBRANE, GOCC_ORGANELLE_SUBCOMPARTMENT, GOCC_GOLGI_CIS_CISTERNA, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, MIR3646, MIR520D_5P, MIR524_5P, MIR19A_3P, MIR19B_3P, MIR4719

GO Biological Process (1): Golgi organization (GO:0007030)

GO Molecular Function (0):

GO Cellular Component (4): Golgi cis cisterna (GO:0000137), cis-Golgi network (GO:0005801), Golgi cisterna membrane (GO:0032580), Golgi apparatus (GO:0005794)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
Golgi cisterna	2
intracellular membrane-bounded organelle	2
organelle organization	1
endomembrane system organization	1
Golgi apparatus	1
organelle membrane	1
cytoplasm	1
endomembrane system	1

Protein interactions and networks

STRING

282 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GOLGA6B	USP17L3	A6NCW0	576
GOLGA6B	NPIPB11	E5RHQ5	507
GOLGA6B	NPIPA5	E9PKD4	507
GOLGA6B	NPIPA3	F8WFD2	506
GOLGA6B	A6NGT6	A6NGT6	478
GOLGA6B	GOLGA7B	Q2TAP0	477
GOLGA6B	RFPL4B	Q6ZWI9	439
GOLGA6B	ARHGAP11B	Q3KRB8	435
GOLGA6B	GOLGA7	Q7Z5G4	382
GOLGA6B	NBPF11	Q86T75	378
GOLGA6B	ZNF705D	P0CH99	370
GOLGA6B	LRRC37A	A6NMS7	368
GOLGA6B	TRIM51	Q9BSJ1	367
GOLGA6B	LRRC37A3	O60309	360
GOLGA6B	NPIPA1	Q9UND3	355

IntAct

2 interactions, top by confidence:

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

BioGRID (3): CLRN3 (Cross-Linking-MS (XL-MS)), DBN1 (Cross-Linking-MS (XL-MS)), GOLGA6B (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A2AM05, A2RUR9, A5D8S1, A6H5Y1, A6NC78, A6NDN3, A6NMD2, A9JSR5, A9ZSY0, D6RF30, H3BQL2, H3BSY2, P0CJ92, Q19UN5, Q3TCJ8, Q3URK1, Q3V036, Q3V125, Q3ZRW6, Q3ZRW7, Q49A88, Q5CZC0, Q5IR70, Q5R6R3, Q5R8Y4, Q5TB80, Q640L3, Q66HB6, Q6AXN6, Q6ZQ06, Q811D2, Q86TE4, Q86V48, Q8BGY3, Q8CDM4, Q8IYA2, Q8K2J4, Q8K389, Q8R4U7, Q8TC20

Diamond homologs: A0A1B0GV03, A1IH00, A6NC78, A6NCC3, A6NDK9, A6NDN3, A6NEF3, A6NEM1, A6NI86, A6NN73, A7E2F4, A8MQT2, A8MZA4, F8WBI6, H0YKK7, H0YM25, H3BPF8, H3BSY2, H3BV12, I6L899, P0CG33, P0CJ92, P0DX00, P0DX01, P0DX02, P0DX52, P0DX53, Q08379, Q62839, Q8N7Z2, Q8N9W4, Q921M4, Q9NYA3, A6NMD2, D6RF30, H3BQL2, Q0D2H9, Q9HBQ8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	99
Likely benign	8
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2708 predictions. Top by Δscore:

Variant	Effect	Δscore
15:72656507:CACA:C	acceptor_loss	1.0000
15:72656508:ACAG:A	acceptor_loss	1.0000
15:72656509:CAG:C	acceptor_loss	1.0000
15:72656510:A:AG	acceptor_gain	1.0000
15:72656510:A:C	acceptor_loss	1.0000
15:72656511:G:GG	acceptor_gain	1.0000
15:72656511:GCT:G	acceptor_gain	1.0000
15:72656511:GCTA:G	acceptor_gain	1.0000
15:72656611:G:GA	donor_gain	1.0000
15:72656627:GGGAT:G	donor_gain	1.0000
15:72656628:GGAT:G	donor_gain	1.0000
15:72656628:GGATG:G	donor_gain	1.0000
15:72656629:G:GT	donor_gain	1.0000
15:72656629:G:T	donor_gain	1.0000
15:72656629:GAT:G	donor_gain	1.0000
15:72656632:G:GG	donor_gain	1.0000
15:72658518:A:AG	acceptor_gain	1.0000
15:72658519:C:G	acceptor_gain	1.0000
15:72658520:A:AG	acceptor_gain	1.0000
15:72658531:A:AG	acceptor_gain	1.0000
15:72658532:A:G	acceptor_gain	1.0000
15:72658548:T:G	acceptor_gain	1.0000
15:72659530:G:GT	donor_gain	1.0000
15:72659533:G:GG	donor_gain	1.0000
15:72659788:CTACA:C	acceptor_loss	1.0000
15:72659789:TACAG:T	acceptor_loss	1.0000
15:72659792:A:G	acceptor_loss	1.0000
15:72660122:GAA:G	acceptor_gain	1.0000
15:72660218:G:GT	donor_gain	1.0000
15:72660226:CAGGG:C	donor_loss	1.0000

AlphaMissense

4558 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:72660020:T:C	F151L	0.882
15:72660022:C:A	F151L	0.882
15:72660022:C:G	F151L	0.882
15:72660128:T:C	S155P	0.863
15:72661811:T:C	L271P	0.861
15:72659958:T:C	L130P	0.855
15:72662357:T:C	L318P	0.853
15:72659979:T:C	L137S	0.849
15:72661493:G:C	R229P	0.847
15:72662324:T:C	L307P	0.842
15:72660150:T:C	L162P	0.836
15:72659972:G:C	A135P	0.814
15:72661472:T:C	L222P	0.809
15:72661536:G:C	W243C	0.808
15:72661536:G:T	W243C	0.808
15:72659794:G:C	A109P	0.803
15:72666041:T:C	F623L	0.800
15:72666043:C:A	F623L	0.800
15:72666043:C:G	F623L	0.800
15:72662314:G:C	A304P	0.787
15:72665665:T:C	F555L	0.780
15:72665667:C:A	F555L	0.780
15:72665667:C:G	F555L	0.780
15:72658616:T:C	L88P	0.779
15:72661534:T:A	W243R	0.778
15:72661534:T:C	W243R	0.778
15:72660011:G:C	A148P	0.775
15:72661468:T:C	S221P	0.773
15:72665602:T:C	F534L	0.768
15:72665604:T:A	F534L	0.768

dbSNP variants (sampled 300 via entrez): RS1000227339 (15:72668204 C>T), RS1000278457 (15:72666835 G>A), RS1000969593 (15:72663088 C>T), RS1004306434 (15:72653050 C>G), RS1006863556 (15:72664268 C>A,T), RS1007220424 (15:72664609 A>G), RS1007608442 (15:72653380 T>C), RS1008482583 (15:72657385 CGGG>C), RS1009213215 (15:72660916 A>G), RS1009265589 (15:72657425 G>A), RS1013004168 (15:72669558 G>A), RS1013110434 (15:72667181 G>A,T), RS1013394022 (15:72663125 C>T), RS1013471840 (15:72668535 G>A), RS1013756367 (15:72663860 C>G)

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

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
2-palmitoylglycerol	increases expression	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

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