GOLGA6L4

Summary

GOLGA6L4 (golgin A6 family like 4, HGNC:27256) is a protein-coding gene on chromosome 15q25.2, encoding Golgin subfamily A member 6-like protein 4 (A6NEF3). It is a common-essential gene (DepMap: required in 100.0% of cancer cell lines).

At a glance

• GWAS associations: 18
• Clinical variants (ClinVar): 2 total
• Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_001267536

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27256
Approved symbol	GOLGA6L4
Name	golgin A6 family like 4
Location	15q25.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000184206
Ensembl biotype	protein_coding
Entrez	643707

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 retained_intron, 2 protein_coding

ENST00000379674, ENST00000510439, ENST00000512109, ENST00000515814

RefSeq mRNA: 1 — MANE Select: NM_001267536 NM_001267536

CCDS: CCDS73774

Canonical transcript exons

ENST00000510439 — 9 exons

Exon	Start	End
ENSE00002056415	84239788	84240782
ENSE00002440031	84237586	84237705
ENSE00002442862	84238328	84238387
ENSE00002447722	84242147	84242249
ENSE00002481572	84241049	84241109
ENSE00002488024	84235773	84235918
ENSE00002493946	84238573	84238653
ENSE00002511459	84239318	84239405
ENSE00003893161	84242460	84245358

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 89.80.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ovary	UBERON:0002119	89.80	gold quality
sural nerve	UBERON:0015488	89.79	gold quality
ovary	UBERON:0000992	88.49	gold quality
right ovary	UBERON:0002118	87.22	gold quality
cortical plate	UBERON:0005343	86.30	gold quality
left testis	UBERON:0004533	86.12	gold quality
right testis	UBERON:0004534	85.34	gold quality
mucosa of stomach	UBERON:0001199	85.23	gold quality
testis	UBERON:0000473	85.15	gold quality
body of uterus	UBERON:0009853	84.23	gold quality
uterine cervix	UBERON:0000002	83.83	gold quality
vagina	UBERON:0000996	83.31	gold quality
ectocervix	UBERON:0012249	83.19	gold quality
endocervix	UBERON:0000458	83.07	gold quality
myometrium	UBERON:0001296	82.76	gold quality
stromal cell of endometrium	CL:0002255	82.50	gold quality
tibial nerve	UBERON:0001323	81.89	gold quality
muscle layer of sigmoid colon	UBERON:0035805	81.66	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	81.52	gold quality
subcutaneous adipose tissue	UBERON:0002190	81.25	gold quality
endometrium	UBERON:0001295	81.19	gold quality
apex of heart	UBERON:0002098	81.17	gold quality
lower esophagus muscularis layer	UBERON:0035833	81.07	gold quality
lower esophagus	UBERON:0013473	81.03	gold quality
left adrenal gland cortex	UBERON:0035825	81.03	gold quality
left uterine tube	UBERON:0001303	80.96	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.83	gold quality
right adrenal gland cortex	UBERON:0035827	80.67	gold quality
right adrenal gland	UBERON:0001233	80.57	gold quality
thoracic mammary gland	UBERON:0005200	80.56	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

135 targeting GOLGA6L4, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
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-3662	99.99	73.82	5684
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
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-568	99.98	69.86	2084
HSA-MIR-5696	99.98	72.36	4487
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

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Cross-species orthologs

0 orthologs

Paralogs (10): GOLGA6L2 (ENSG00000174450), GOLGA6L9 (ENSG00000197978), 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 4 — A6NEF3 (reviewed: A6NEF3)

All UniProt accessions (2): A6NEF3, H0YA86

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the GOLGA6 family.

RefSeq proteins (1): NP_001254465* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026737	GOLGA6L	Family
IPR043976	GOLGA_cons_dom	Domain

Pfam: PF15070

UniProt features (8 total): compositionally biased region 4, region of interest 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NEF3-F1	76.86	0.50

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): WHITFIELD_CELL_CYCLE_S, MIR607, MIR3646, MIR335_3P, MIR520D_5P, MIR524_5P, MIR4262, MIR181A_5P_MIR181B_5P, MIR181D_5P, MIR181C_5P, MIR4719, MIR4672, MIR4500, MIR6844, MIR543

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

114 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GOLGA6L4	TRAPPC12	Q8WVT3	435
GOLGA6L4	PHF7	Q9BWX1	400
GOLGA6L4	BAIAP3	O94812	373
GOLGA6L4	ADAMTSL3	P82987	366
GOLGA6L4	ZNF431	Q8TF32	358
GOLGA6L4	ZDHHC3	Q9NYG2	321
GOLGA6L4	FUT1	P19526	298
GOLGA6L4	ADCY2	Q08462	290
GOLGA6L4	TGIF2	Q9GZN2	290
GOLGA6L4	NBPF20	P0DPF2	290
GOLGA6L4	SHKBP1	Q8TBC3	287
GOLGA6L4	KLHL33	A6NCF5	272
GOLGA6L4	ZNF714	Q96N38	269
GOLGA6L4	MAP6D1	Q9H9H5	264
GOLGA6L4	KRT37	O76014	248

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0J9YWL9, A0A0J9YY54, A5D7L8, A6NEF3, A6NI86, B2KFW1, B4DH59, D3YZV8, E9Q6E9, F1LWT0, F6QRE9, H0YKK7, O15069, P17040, P17564, P21263, P51843, P62521, P79386, Q0P6D6, Q13342, Q2EG98, Q2KI51, Q3BBV2, Q4VC44, Q5F378, Q5QGU6, Q63560, Q6ITT4, Q6P5H2, Q6ZQX7, Q86T75, Q8CHD8, Q8IWY8, Q8N660, Q8N693, Q99PG2, Q9BE18, Q9BG93, Q9BG94

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

2 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	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1140 predictions. Top by Δscore:

Variant	Effect	Δscore
15:84237581:CACA:C	acceptor_loss	1.0000
15:84237582:ACAGT:A	acceptor_loss	1.0000
15:84237583:CA:C	acceptor_loss	1.0000
15:84237584:A:AG	acceptor_gain	1.0000
15:84237584:AGTT:A	acceptor_loss	1.0000
15:84237585:G:GA	acceptor_gain	1.0000
15:84237585:GT:G	acceptor_gain	1.0000
15:84237585:GTT:G	acceptor_gain	1.0000
15:84237585:GTTA:G	acceptor_gain	1.0000
15:84237585:GTTAA:G	acceptor_gain	1.0000
15:84237701:GGGAT:G	donor_gain	1.0000
15:84237702:GGAT:G	donor_gain	1.0000
15:84237702:GGATG:G	donor_gain	1.0000
15:84237703:G:T	donor_gain	1.0000
15:84237703:GAT:G	donor_gain	1.0000
15:84237703:GATG:G	donor_gain	1.0000
15:84237705:TG:T	donor_loss	1.0000
15:84237706:G:GA	donor_loss	1.0000
15:84237706:G:GG	donor_gain	1.0000
15:84237707:TGAG:T	donor_loss	1.0000
15:84237708:G:GG	donor_loss	1.0000
15:84238323:TGCA:T	acceptor_loss	1.0000
15:84238324:GCA:G	acceptor_loss	1.0000
15:84238325:CAG:C	acceptor_loss	1.0000
15:84238326:A:AG	acceptor_gain	1.0000
15:84238326:A:C	acceptor_loss	1.0000
15:84238327:G:GT	acceptor_gain	1.0000
15:84238327:GT:G	acceptor_gain	1.0000
15:84238327:GTC:G	acceptor_gain	1.0000
15:84238533:A:AG	acceptor_gain	1.0000

AlphaMissense

3732 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:84237587:T:C	L29S	0.956
15:84235912:G:C	K26N	0.941
15:84235912:G:T	K26N	0.941
15:84240731:G:C	W459C	0.925
15:84240731:G:T	W459C	0.925
15:84239860:T:C	L169P	0.920
15:84239893:T:C	L180P	0.919
15:84239872:T:C	L173P	0.911
15:84240729:T:A	W459R	0.891
15:84240729:T:C	W459R	0.891
15:84237595:T:G	Y32D	0.886
15:84237591:A:C	K30N	0.880
15:84237591:A:T	K30N	0.880
15:84235873:G:A	M13I	0.877
15:84235873:G:C	M13I	0.877
15:84235873:G:T	M13I	0.877
15:84235907:G:C	A25P	0.869
15:84240771:T:C	F473L	0.864
15:84240773:C:A	F473L	0.864
15:84240773:C:G	F473L	0.864
15:84237595:T:C	Y32H	0.862
15:84235908:C:A	A25D	0.858
15:84235838:T:A	W2R	0.854
15:84235838:T:C	W2R	0.854
15:84237595:T:A	Y32N	0.853
15:84240718:T:C	L455P	0.853
15:84239384:T:C	F138L	0.848
15:84239386:C:A	F138L	0.848
15:84239386:C:G	F138L	0.848
15:84240706:T:C	L451P	0.844

dbSNP variants (sampled 300 via entrez): RS1000037950 (15:84245258 G>C), RS1000408651 (15:84243507 T>A), RS1001216502 (15:84242909 G>A), RS1001581120 (15:84240631 A>G), RS1006464593 (15:84240528 G>A), RS1009834565 (15:84245110 A>G), RS1016371454 (15:84240621 C>A,T), RS1018200838 (15:84243522 C>A), RS1018523902 (15:84245299 T>A), RS1020071020 (15:84241809 G>A), RS1020098508 (15:84243460 A>T), RS1035416946 (15:84240697 T>A,G), RS1035510767 (15:84235498 T>C), RS1039137762 (15:84239384 T>C), RS1039640844 (15:84234722 C>A,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

18 associations (top):

Study	Trait	p-value
GCST002539_78	Schizophrenia	2.000000e-11
GCST004521_253	Autism spectrum disorder or schizophrenia	6.000000e-11
GCST006803_69	Schizophrenia	9.000000e-10
GCST008103_25	Bipolar disorder	3.000000e-08
GCST012226_535	Waist circumference adjusted for body mass index	2.000000e-14
GCST012226_536	Waist circumference adjusted for body mass index	4.000000e-17
GCST012227_327	Hip circumference adjusted for BMI	3.000000e-08
GCST012227_328	Hip circumference adjusted for BMI	6.000000e-10
GCST012231_131	A body shape index	4.000000e-09
GCST012231_132	A body shape index	3.000000e-09
GCST90020024_732	A body shape index	2.000000e-09
GCST90020024_733	A body shape index	4.000000e-08
GCST90020028_1359	Hip circumference adjusted for BMI	9.000000e-16
GCST90020028_1360	Hip circumference adjusted for BMI	2.000000e-15
GCST90020028_1361	Hip circumference adjusted for BMI	2.000000e-10
GCST90020029_762	Waist circumference adjusted for body mass index	2.000000e-15
GCST90020029_763	Waist circumference adjusted for body mass index	2.000000e-20
GCST90020029_764	Waist circumference adjusted for body mass index	5.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007789	BMI-adjusted waist circumference
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Copper	affects cotreatment, decreases expression	1
Testosterone	increases expression	1

Clinical trials (associated diseases)

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