GOLGA6A

Summary

GOLGA6A (golgin A6 family member A, HGNC:13567) is a protein-coding gene on chromosome 15q24.1, encoding Golgin subfamily A member 6A (Q9NYA3). It is a selective cancer dependency (DepMap: 80.0% of cell lines).

The Golgi apparatus, which participates in glycosylation and transport of proteins and lipids in the secretory pathway, consists of a series of stacked cisternae (flattened membrane sacs). Interactions between the Golgi and microtubules are thought to be important for the reorganization of the Golgi after it fragments during mitosis. The protein encoded by this gene is a member of the golgin family of proteins, whose members localize to the Golgi. This gene is found in a large, low copy repeat sequence or duplicon that is found in multiple copies, that are greather than 90% similar, on chromosome 15. Duplicons are associated with deletions, inversions and other chromosome rearrangements that underlie genomic disease. The protein encoded by this gene is thought to be a functional golgin protein while the majority of the related copies of this gene are thought to be transcribed pseudogenes.

Source: NCBI Gene 342096 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 97 total
• Cancer dependency (DepMap): dependent in 80.0% of screened cell lines
• MANE Select transcript: NM_001038640

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13567
Approved symbol	GOLGA6A
Name	golgin A6 family member A
Location	15q24.1
Locus type	gene with protein product
Status	Approved
Aliases	GLP
Ensembl gene	ENSG00000159289
Ensembl biotype	protein_coding
OMIM	610288
Entrez	342096

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 retained_intron, 1 protein_coding

ENST00000290438, ENST00000562157, ENST00000568723, ENST00000569486

RefSeq mRNA: 1 — MANE Select: NM_001038640 NM_001038640

CCDS: CCDS32290

Canonical transcript exons

ENST00000290438 — 18 exons

Exon	Start	End
ENSE00001520671	74069857	74071037
ENSE00002435022	74071554	74071656
ENSE00002443081	74075683	74075790
ENSE00002446529	74080616	74080735
ENSE00002475890	74071124	74071277
ENSE00002480084	74071367	74071470
ENSE00002484842	74075899	74075985
ENSE00002505186	74077221	74077302
ENSE00002506433	74077403	74077453
ENSE00002513464	74074148	74074216
ENSE00002518337	74074493	74075001
ENSE00002518970	74077018	74077124
ENSE00002519842	74072218	74072309
ENSE00002528542	74075403	74075490
ENSE00002536046	74072742	74072817
ENSE00003463889	74078609	74078689
ENSE00003553238	74077715	74077753
ENSE00003677229	74082426	74082550

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 88.31.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	88.31	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.54	gold quality
left testis	UBERON:0004533	87.44	gold quality
testis	UBERON:0000473	87.05	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.25	gold quality
apex of heart	UBERON:0002098	67.58	gold quality
liver	UBERON:0002107	66.42	gold quality
right lobe of liver	UBERON:0001114	60.95	gold quality
stromal cell of endometrium	CL:0002255	55.36	gold quality
cerebellum	UBERON:0002037	54.69	gold quality
cerebellar cortex	UBERON:0002129	54.45	gold quality
sural nerve	UBERON:0015488	54.19	silver quality
cerebellar hemisphere	UBERON:0002245	54.12	gold quality
muscle of leg	UBERON:0001383	54.11	gold quality
skeletal muscle organ	UBERON:0014892	54.00	gold quality
gastrocnemius	UBERON:0001388	53.54	gold quality
right uterine tube	UBERON:0001302	52.97	gold quality
right hemisphere of cerebellum	UBERON:0014890	52.95	gold quality
skeletal muscle tissue	UBERON:0001134	50.81	gold quality
mucosa of stomach	UBERON:0001199	50.68	gold quality
tibial artery	UBERON:0007610	50.11	gold quality
popliteal artery	UBERON:0002250	50.07	gold quality
fallopian tube	UBERON:0003889	49.04	gold quality
peripheral nervous system	UBERON:0000010	48.98	gold quality
tibial nerve	UBERON:0001323	48.98	gold quality
left lobe of thyroid gland	UBERON:0001120	48.89	gold quality
left uterine tube	UBERON:0001303	48.01	gold quality
body of uterus	UBERON:0009853	48.01	gold quality
superior frontal gyrus	UBERON:0002661	47.88	gold quality
ectocervix	UBERON:0012249	47.63	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

62 targeting GOLGA6A, 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-4267	99.96	66.53	2368
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-3682-3P	99.58	67.63	865
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-1272	99.34	68.79	878

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 80.0% of screened cell lines.

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), GOLGA2 (ENSG00000167110), GOLGA6C (ENSG00000167195), GOLGA8A (ENSG00000175265), GOLGA8Q (ENSG00000178115), GOLGA8J (ENSG00000179938), GOLGA8G (ENSG00000183629), GOLGA8R (ENSG00000186399), GOLGA8M (ENSG00000188626), GOLGA8O (ENSG00000206127), GOLGA6B (ENSG00000215186), GOLGA8B (ENSG00000215252), GOLGA8N (ENSG00000232653), GOLGA8K (ENSG00000249931), GOLGA8T (ENSG00000261247), GOLGA8S (ENSG00000261739), GOLGA8H (ENSG00000261794)

Protein

Protein identifiers

Golgin subfamily A member 6A — Q9NYA3 (reviewed: Q9NYA3)

Alternative names: Golgin linked to PML, Golgin-like protein

All UniProt accessions (1): Q9NYA3

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Highly expressed in seminiferous tubes in testis. Highly expressed in spermatids, barely detectable in late pachytene spermatocytes, and not detectable in spermatogonia. Detected at intermediate levels in pancreas and lymph nodes, and at much lower levels in spleen, peripheral blood leukocytes, skeletal muscle, liver, lung, placenta, brain and heart.

Similarity. Belongs to the GOLGA6 family.

RefSeq proteins (1): NP_001033729* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024858	GOLGA	Family
IPR043976	GOLGA_cons_dom	Domain

Pfam: PF15070

UniProt features (14 total): sequence conflict 5, region of interest 3, compositionally biased region 3, chain 1, coiled-coil region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NYA3-F1	74.20	0.47

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 39 (showing top): TGIF_01, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_GOLGI_ORGANIZATION, GOCC_GOLGI_STACK, GOCC_GOLGI_CISTERNA, GOCC_CIS_GOLGI_NETWORK, GOCC_GOLGI_CISTERNA_MEMBRANE, GOCC_ORGANELLE_SUBCOMPARTMENT, DUAN_PRDM5_TARGETS, GOCC_GOLGI_CIS_CISTERNA, MIR3646, MIR520D_5P, MIR524_5P, MIR19A_3P, MIR19B_3P

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

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

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
binding	1
Golgi apparatus	1
organelle membrane	1
cytoplasm	1
endomembrane system	1

Protein interactions and networks

STRING

410 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GOLGA6A	ISLR2	Q6UXK2	507
GOLGA6A	GAGE12H	A6NDE8	447
GOLGA6A	UBL7	Q96S82	443
GOLGA6A	BNIP5	P0C671	418
GOLGA6A	CCDC33	Q8N5R6	418
GOLGA6A	GOLGA7B	Q2TAP0	415
GOLGA6A	LRRC37A	A6NMS7	397
GOLGA6A	NPIPB6	E9PJ23	396
GOLGA6A	NUP205	Q92621	395
GOLGA6A	FAM219B	Q5XKK7	393
GOLGA6A	STOML1	Q9UBI4	380
GOLGA6A	PRMT2IP	Q6ZRI6	368
GOLGA6A	RIN3	Q8TB24	358
GOLGA6A	ZNF821	O75541	358
GOLGA6A	LRRC37B	Q96QE4	338

IntAct

142 interactions, top by confidence:

A	B	Type	Score
KCTD9	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.670
YJU2	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
KIF9	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
MYOZ1	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
UTP14C	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6A	BAG5	psi-mi:“MI:0915”(physical association)	0.560
MGC50722	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
KANK2	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
PPP2R1A	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
NEBL	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
MKRN3	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
KLHL38	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
TXLNA	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
ELOA	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
MAPK9	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
SYT17	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
POLR1C	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
DEF6	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6A	USP15	psi-mi:“MI:0915”(physical association)	0.560
ZC2HC1C	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
KDM1A	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
MYOZ3	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
SPATC1L	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
DUSP29	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
USP2	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
PSMA1	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
TTC5	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
TRAPPC6A	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
CDC7	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560
FHL2	GOLGA6A	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (58): GOLGA6A (Affinity Capture-MS), GOLGA6A (Two-hybrid), GOLGA6A (Two-hybrid), GOLGA6A (Two-hybrid), GOLGA6A (Two-hybrid), GOLGA6A (Two-hybrid), GOLGA6A (Two-hybrid), GOLGA6A (Two-hybrid), GOLGA6A (Two-hybrid), GOLGA6A (Two-hybrid), GOLGA6A (Two-hybrid), GOLGA6A (Two-hybrid), GOLGA6A (Two-hybrid), GOLGA6A (Two-hybrid), GOLGA6A (Two-hybrid)

ESM2 similar proteins: A2AM05, A6NC78, A6NCC3, A6NDK9, A6NDN3, A6NJZ7, A6NMD2, A6NN73, A6NNM3, A7E2F4, A8MQT2, D6RF30, F8WBI6, H3BPF8, H3BQL2, H3BSY2, H3BV12, I6L899, P0CG33, P0CJ92, P0DO97, P0DX52, P0DX53, P54257, Q0D2H9, Q0KK56, Q2M243, Q3T1I3, Q3TCJ8, Q3V0F0, Q5BK57, Q5XHZ2, Q6AW69, Q6AXN6, Q6PHN1, Q7TME2, Q8BG89, Q8BGY3, Q8C0G2, Q8K389

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	82
Likely benign	15
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2954 predictions. Top by Δscore:

Variant	Effect	Δscore
15:74071033:AAAAA:A	acceptor_gain	1.0000
15:74071035:AAA:A	acceptor_gain	1.0000
15:74071038:C:CC	acceptor_gain	1.0000
15:74071119:CTCA:C	donor_loss	1.0000
15:74071120:TCACC:T	donor_loss	1.0000
15:74071121:CACCA:C	donor_loss	1.0000
15:74071122:A:AC	donor_gain	1.0000
15:74071122:AC:A	donor_gain	1.0000
15:74071122:ACCAT:A	donor_gain	1.0000
15:74071123:C:CC	donor_gain	1.0000
15:74071123:C:CG	donor_loss	1.0000
15:74071123:CC:C	donor_gain	1.0000
15:74071123:CCAT:C	donor_gain	1.0000
15:74071123:CCATC:C	donor_gain	1.0000
15:74071275:CAC:C	acceptor_gain	1.0000
15:74071276:AC:A	acceptor_gain	1.0000
15:74071277:CC:C	acceptor_gain	1.0000
15:74071278:C:CC	acceptor_gain	1.0000
15:74071363:CTA:C	donor_loss	1.0000
15:74071364:TACCT:T	donor_loss	1.0000
15:74071365:A:AC	donor_gain	1.0000
15:74071366:C:CC	donor_gain	1.0000
15:74071366:CCTT:C	donor_gain	1.0000
15:74071377:T:TA	donor_gain	1.0000
15:74071466:CTCTC:C	acceptor_gain	1.0000
15:74071468:CTC:C	acceptor_gain	1.0000
15:74071469:TCCTG:T	acceptor_loss	1.0000
15:74071471:C:CC	acceptor_gain	1.0000
15:74071471:CT:C	acceptor_loss	1.0000
15:74071472:T:G	acceptor_loss	1.0000

AlphaMissense

4559 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:74077225:G:C	F151L	0.877
15:74077225:G:T	F151L	0.877
15:74077227:A:G	F151L	0.877
15:74075438:A:G	L271P	0.869
15:74074929:A:G	L307P	0.868
15:74075756:C:G	R229P	0.861
15:74074896:A:G	L318P	0.855
15:74075713:C:A	W243C	0.851
15:74075713:C:G	W243C	0.851
15:74077268:A:G	L137S	0.850
15:74077289:A:G	L130P	0.843
15:74077119:A:G	S155P	0.842
15:74075715:A:G	W243R	0.841
15:74075715:A:T	W243R	0.841
15:74078631:A:G	L88P	0.837
15:74074939:C:G	A304P	0.825
15:74077453:C:G	A109P	0.825
15:74077097:A:G	L162P	0.815
15:74077275:C:G	A135P	0.810
15:74071648:A:C	F534L	0.795
15:74071648:A:T	F534L	0.795
15:74071650:A:G	F534L	0.795
15:74075777:A:G	L222P	0.793
15:74075781:A:G	S221P	0.778
15:74071209:G:C	F623L	0.774
15:74071209:G:T	F623L	0.774
15:74071211:A:G	F623L	0.774
15:74075714:C:G	W243S	0.757
15:74077109:A:G	L158P	0.743
15:74077280:T:A	E133V	0.739

dbSNP variants (sampled 300 via entrez): RS1011419714 (15:74079295 A>C,T), RS1022729226 (15:74073240 C>T), RS1022760295 (15:74080088 A>G), RS1030756753 (15:74071479 G>A), RS1031620802 (15:74072867 C>A,T), RS1032737989 (15:74078394 G>A,C), RS1035475246 (15:74080254 T>C,G), RS1039204030 (15:74071315 G>A), RS1039234757 (15:74077856 A>G), RS1047935600 (15:74071182 A>G), RS1051896472 (15:74078024 A>G), RS1052350317 (15:74084293 T>C,G), RS111502901 (15:74082329 G>A), RS111619831 (15:74075211 G>A), RS111623847 (15:74083554 T>G)

Disease associations

OMIM: gene MIM:610288 | 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

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

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
methylmercuric chloride	affects reaction, increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	decreases methylation	1
theaflavin-3,3’-digallate	affects expression	1
Benzo(a)pyrene	affects methylation	1
Diethylhexyl Phthalate	decreases expression	1
Methapyrilene	decreases methylation	1
Smoke	decreases expression	1
Aflatoxin B1	increases expression	1

Clinical trials (associated diseases)

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