GOLGA6L9

Summary

GOLGA6L9 (golgin A6 family like 9, HGNC:37229) is a protein-coding gene on chromosome 15q25.2, encoding Golgin subfamily A member 6-like protein 9 (A6NEM1). It is a selective cancer dependency (DepMap: 20.0% of cell lines).

At a glance

• GWAS associations: 1
• Cancer dependency (DepMap): dependent in 20.0% of screened cell lines
• MANE Select transcript: NM_198181

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37229
Approved symbol	GOLGA6L9
Name	golgin A6 family like 9
Location	15q25.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000197978
Ensembl biotype	protein_coding
Entrez	440295

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 retained_intron, 1 protein_coding

ENST00000558668, ENST00000618348, ENST00000618706

RefSeq mRNA: 2 — MANE Select: NM_198181 NM_001291420, NM_198181

CCDS: CCDS45326

Canonical transcript exons

ENST00000618348 — 9 exons

Exon	Start	End
ENSE00003720108	82435967	82436069
ENSE00003722840	82432817	82432897
ENSE00003727034	82434869	82434929
ENSE00003732296	82436279	82439153
ENSE00003737493	82432572	82432631
ENSE00003738492	82434034	82434602
ENSE00003738544	82431830	82431949
ENSE00003752807	82433562	82433649
ENSE00003924820	82429816	82430163

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 88.22.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	88.22	gold quality
right uterine tube	UBERON:0001302	88.05	gold quality
esophagus mucosa	UBERON:0002469	86.07	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.49	gold quality
vagina	UBERON:0000996	82.86	gold quality
minor salivary gland	UBERON:0001830	82.66	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.42	gold quality
saliva-secreting gland	UBERON:0001044	81.98	gold quality
endometrium	UBERON:0001295	81.91	gold quality
esophagus	UBERON:0001043	81.00	gold quality
cortical plate	UBERON:0005343	80.64	gold quality
ectocervix	UBERON:0012249	80.23	gold quality
left ovary	UBERON:0002119	80.20	gold quality
ganglionic eminence	UBERON:0004023	79.83	gold quality
uterine cervix	UBERON:0000002	79.47	gold quality
body of stomach	UBERON:0001161	79.25	gold quality
fundus of stomach	UBERON:0001160	79.16	gold quality
ovary	UBERON:0000992	79.07	gold quality
body of pancreas	UBERON:0001150	78.74	gold quality
body of uterus	UBERON:0009853	78.72	gold quality
right ovary	UBERON:0002118	78.16	gold quality
ventricular zone	UBERON:0003053	78.12	gold quality
left testis	UBERON:0004533	77.83	gold quality
testis	UBERON:0000473	77.76	gold quality
myometrium	UBERON:0001296	77.74	gold quality
muscle layer of sigmoid colon	UBERON:0035805	77.58	gold quality
stomach	UBERON:0000945	77.27	gold quality
endocervix	UBERON:0000458	77.03	gold quality
right testis	UBERON:0004534	76.79	gold quality
skin of abdomen	UBERON:0001416	76.54	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.81
E-MTAB-7249	no	237.77

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

118 targeting GOLGA6L9, 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-4262	100.00	73.26	3931
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-8068	99.98	73.85	2376
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-607	99.97	73.62	5593
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-7-1-3P	99.91	71.53	4384

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 20.0% of screened cell lines.

Cross-species orthologs

0 orthologs

Paralogs (10): GOLGA6L2 (ENSG00000174450), GOLGA6L4 (ENSG00000184206), GOLGA6L25 (ENSG00000227717), GOLGA6L24 (ENSG00000237850), GOLGA6L7 (ENSG00000261649), GOLGA6L26 (ENSG00000273756), GOLGA6L1 (ENSG00000273976), GOLGA6L6 (ENSG00000277322), GOLGA6L22 (ENSG00000277865), GOLGA6L10 (ENSG00000278662)

Protein

Protein identifiers

Golgin subfamily A member 6-like protein 9 — A6NEM1 (reviewed: A6NEM1)

All UniProt accessions (1): A6NEM1

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the GOLGA6 family.

Isoforms (2)

UniProt ID	Names	Canonical?
A6NEM1-1	1	yes
A6NEM1-2	2

RefSeq proteins (2): NP_001278349, NP_937824* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026737	GOLGA6L	Family
IPR043976	GOLGA_cons_dom	Domain

Pfam: PF15070

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NEM1-F1	74.87	0.45

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 30 (showing top): TGIF_01, CAGTATT_MIR200B_MIR200C_MIR429, MIR607, MIR3646, MIR335_3P, MIR4262, MIR7_1_3P, MIR7_2_3P, MIR4719, MIR3133, MIR6844, MIR543, MIR1303, MIR302A_5P, MIR5701

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

593 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GOLGA6L9	USP17L18	D6R9N7	692
GOLGA6L9	USP17L11	C9JVI0	621
GOLGA6L9	OR8K3	Q8NH51	520
GOLGA6L9	ATAD3C	Q5T2N8	447
GOLGA6L9	MEGF6	O75095	375
GOLGA6L9	FBXO17	Q96EF6	370
GOLGA6L9	PIK3R6	Q5UE93	370
GOLGA6L9	FRMD6	Q96NE9	369
GOLGA6L9	DNAH6	Q9C0G6	363
GOLGA6L9	INHBE	P58166	302
GOLGA6L9	MUC19	Q7Z5P9	302
GOLGA6L9	PRR19	A6NJB7	301
GOLGA6L9	TMEM145	Q8NBT3	294
GOLGA6L9	SH2D4B	Q5SQS7	290
GOLGA6L9	AHNAK2	Q8IVF2	283

IntAct

656 interactions, top by confidence:

A	B	Type	Score
DISC1	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
POLL	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
CDC37	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
HGS	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
JRK	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
USHBP1	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
ZNF444	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
ZNF410	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
TSEN54	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
WDR25	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
ZNF329	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
CCDC146	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
PATZ1	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
ZKSCAN3	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
PRPF31	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
ZNF417	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
ZNF438	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
ZNF844	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
ZNF414	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
GOLGA6L9	ZNF628	psi-mi:“MI:0915”(physical association)	0.000
DEF6	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
ZNF574	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
ZNF80	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
ZNF578	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
DENND5A	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
UBL4B	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
TPRX1	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
VEZF1	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
GEM	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
TTC23	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (218): GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid), GOLGA6L9 (Two-hybrid)

ESM2 similar proteins: A0A0J9YWL9, A0A0J9YY54, A0A1B0GV03, A6NEF3, A6NEM1, A6NI86, A8MZA4, B4DH59, D3YVF0, F6QRE9, H0YKK7, H0YM25, P0C6Y7, P0C7A2, P0DX00, P0DX01, P0DX02, P14590, P21263, P22793, P24587, P24710, P48997, P48998, Q07283, Q0II65, Q0P6D6, Q13342, Q3BBV2, Q4R9C9, Q5W0A0, Q6AXX0, Q6NSX1, Q6P5H2, Q6P902, Q86T75, Q8CHD8, Q8N2N9, Q8N660, Q8N7Z2

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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1277 predictions. Top by Δscore:

Variant	Effect	Δscore
15:82431828:A:AG	acceptor_gain	1.0000
15:82431829:G:GG	acceptor_gain	1.0000
15:82431945:GGGAT:G	donor_gain	1.0000
15:82431946:GGAT:G	donor_gain	1.0000
15:82431946:GGATG:G	donor_gain	1.0000
15:82431947:G:GT	donor_gain	1.0000
15:82431947:G:T	donor_gain	1.0000
15:82431947:GAT:G	donor_gain	1.0000
15:82431950:G:GG	donor_gain	1.0000
15:82432778:C:G	acceptor_gain	1.0000
15:82432779:A:AG	acceptor_gain	1.0000
15:82432790:A:AG	acceptor_gain	1.0000
15:82432791:A:G	acceptor_gain	1.0000
15:82432806:A:AG	acceptor_gain	1.0000
15:82432807:T:G	acceptor_gain	1.0000
15:82433550:T:TA	acceptor_gain	1.0000
15:82433556:G:A	acceptor_gain	1.0000
15:82433557:GGCA:G	acceptor_loss	1.0000
15:82433558:GCAG:G	acceptor_loss	1.0000
15:82433560:AGG:A	acceptor_loss	1.0000
15:82433645:GACGG:G	donor_gain	1.0000
15:82433648:GG:G	donor_gain	1.0000
15:82433649:GG:G	donor_gain	1.0000
15:82434599:GCTG:G	donor_gain	1.0000
15:82434601:TGG:T	donor_loss	1.0000
15:82434603:G:C	donor_loss	1.0000
15:82434603:G:GG	donor_gain	1.0000
15:82434604:T:G	donor_loss	1.0000
15:82434865:CCAG:C	acceptor_loss	1.0000
15:82434866:CAGA:C	acceptor_loss	1.0000

AlphaMissense

2800 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:82434551:G:C	W317C	0.890
15:82434551:G:T	W317C	0.890
15:82434591:T:C	F331L	0.862
15:82434593:C:A	F331L	0.862
15:82434593:C:G	F331L	0.862
15:82434549:T:A	W317R	0.847
15:82434549:T:C	W317R	0.847
15:82434364:T:C	L255P	0.844
15:82434526:T:C	L309P	0.844
15:82434442:T:C	L281P	0.833
15:82430157:G:C	K26N	0.823
15:82430157:G:T	K26N	0.823
15:82434139:T:C	L180P	0.821
15:82434517:T:C	L306P	0.815
15:82434538:T:C	L313P	0.809
15:82431831:T:C	L29S	0.805
15:82430083:T:A	W2R	0.799
15:82430083:T:C	W2R	0.799
15:82434106:T:C	L169P	0.782
15:82434536:G:A	M312I	0.771
15:82434536:G:C	M312I	0.771
15:82434536:G:T	M312I	0.771
15:82434546:G:T	G316W	0.760
15:82430118:G:A	M13I	0.759
15:82430118:G:C	M13I	0.759
15:82430118:G:T	M13I	0.759
15:82436367:T:C	F419L	0.754
15:82436369:T:A	F419L	0.754
15:82436369:T:G	F419L	0.754
15:82434118:T:C	L173P	0.742

dbSNP variants (sampled 300 via entrez): RS1010969833 (15:82438659 AC>A), RS1012182805 (15:82438551 G>C), RS1012544001 (15:82438289 G>A,C,T), RS1024987796 (15:82438294 T>G), RS1026771798 (15:82438214 A>C), RS1029186642 (15:82438675 C>T), RS1030968698 (15:82438605 A>C), RS1031126507 (15:82438390 A>G,T), RS1036763552 (15:82438202 C>T), RS1046774457 (15:82438565 A>C,G), RS1047756 (15:82438395 T>C,G), RS1048222169 (15:82438509 ATTTG>A), RS1048498279 (15:82419424 G>A,T), RS1049415337 (15:82438026 CAGTTT>C), RS1063299 (15:82438372 C>T)

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

1 associations (top):

Study	Trait	p-value
GCST007277_21	Tourette syndrome	7.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, decreases expression	1
bisphenol A	affects cotreatment, decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
bisphenol S	decreases expression, affects cotreatment	1
Cadmium	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Silicon Dioxide	increases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Urethane	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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