GOLGA6C

Summary

GOLGA6C (golgin A6 family member C, HGNC:32206) is a protein-coding gene on chromosome 15q24.2, encoding Golgin subfamily A member 6C (A6NDK9).

Predicted to be involved in Golgi organization. Predicted to be located in Golgi apparatus. Predicted to be active in Golgi cis cisterna; Golgi cisterna membrane; and cis-Golgi network.

Source: NCBI Gene 653641 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 130 total
• MANE Select transcript: NM_001164404

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32206
Approved symbol	GOLGA6C
Name	golgin A6 family member C
Location	15q24.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000167195
Ensembl biotype	protein_coding
Entrez	653641

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000300576

RefSeq mRNA: 3 — MANE Select: NM_001164404 NM_001164404, NM_001422025, NM_001422030

CCDS: CCDS58388

Canonical transcript exons

ENST00000300576 — 18 exons

Exon	Start	End
ENSE00002316684	75270072	75273455
ENSE00002453526	75266105	75266613
ENSE00002454607	75266890	75266958
ENSE00002457909	75263799	75263880
ENSE00002461260	75265617	75265704
ENSE00002469919	75268797	75268888
ENSE00002474440	75269639	75269742
ENSE00002478202	75265317	75265424
ENSE00002479241	75269832	75269985
ENSE00002480221	75263348	75263386
ENSE00002491457	75260373	75260492
ENSE00002493303	75263648	75263698
ENSE00002496450	75262412	75262492
ENSE00002507372	75269453	75269555
ENSE00002511394	75263977	75264083
ENSE00002516016	75268289	75268364
ENSE00002530078	75265122	75265208
ENSE00003929812	75258334	75258682

Expression profiles

Bgee: expression breadth broad, 17 present calls, max score 82.55.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.55	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.69	silver quality
right testis	UBERON:0004534	72.45	gold quality
testis	UBERON:0000473	70.77	gold quality
left testis	UBERON:0004533	70.73	gold quality
sural nerve	UBERON:0015488	53.98	silver quality
ventricular zone	UBERON:0003053	43.34	gold quality
skeletal muscle tissue	UBERON:0001134	42.99	gold quality
muscle tissue	UBERON:0002385	40.82	gold quality
bone marrow cell	CL:0002092	40.29	gold quality
ganglionic eminence	UBERON:0004023	39.24	silver quality
descending thoracic aorta	UBERON:0002345	38.90	silver quality
duodenum	UBERON:0002114	38.34	silver quality
bone marrow	UBERON:0002371	37.43	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
muscle of leg	UBERON:0001383	36.80	gold quality
liver	UBERON:0002107	36.47	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.48	gold quality
granulocyte	CL:0000094	34.97	gold quality
smooth muscle tissue	UBERON:0001135	34.97	silver quality
gastrocnemius	UBERON:0001388	34.42	gold quality
tibial artery	UBERON:0007610	33.47	gold quality
popliteal artery	UBERON:0002250	33.33	gold quality
prefrontal cortex	UBERON:0000451	33.03	gold quality
vermiform appendix	UBERON:0001154	32.18	gold quality
tonsil	UBERON:0002372	31.81	gold quality
gall bladder	UBERON:0002110	31.06	gold quality
superior frontal gyrus	UBERON:0002661	30.56	gold quality
urinary bladder	UBERON:0001255	30.27	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

134 targeting GOLGA6C, 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-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-4262	100.00	73.26	3931
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-6077	99.99	68.04	2299
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-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955

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), 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 6C — A6NDK9 (reviewed: A6NDK9)

All UniProt accessions (1): A6NDK9

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the GOLGA6 family.

RefSeq proteins (3): NP_001157876, NP_001408954, NP_001408959 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024858	GOLGA	Family
IPR043976	GOLGA_cons_dom	Domain

Pfam: PF15070

UniProt features (7 total): region of interest 3, compositionally biased region 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NDK9-F1	74.79	0.49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 38 (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, MIR520D_5P, MIR524_5P, MIR30B_5P_MIR30C_5P, MIR30D_5P, MIR30E_5P, MIR30A_5P, MIR4729

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

144 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GOLGA6C	ANKRD20A2P	Q5SQ80	725
GOLGA6C	C2orf42	Q9NWW7	720
GOLGA6C	SCGB1D1	O95968	571
GOLGA6C	IPPK	Q9H8X2	526
GOLGA6C	ADGRB3	O60242	419
GOLGA6C	NLRC5	Q86WI3	322
GOLGA6C	AVPR2	P30518	322
GOLGA6C	WDR33	Q9C0J8	248
GOLGA6C	ITSN2	Q9NZM3	238
GOLGA6C	CPSF1	Q10570	207
GOLGA6C	NUDT21	O43809	201
GOLGA6C	CPSF3	Q9UKF6	200
GOLGA6C	CSTF2	P33240	195
GOLGA6C	CPSF4	O95639	189
GOLGA6C	CPSF6	Q16630	176

IntAct

3 interactions, top by confidence:

A	B	Type	Score
GSK3A	GOLGA6C	psi-mi:“MI:0915”(physical association)	0.370
M		psi-mi:“MI:0914”(association)	0.350

BioGRID (3): GOLGA6C (Two-hybrid), CLRN3 (Cross-Linking-MS (XL-MS)), DBN1 (Cross-Linking-MS (XL-MS))

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	117
Likely benign	5
Benign	7

Top pathogenic / likely-pathogenic (0)

SpliceAI

2844 predictions. Top by Δscore:

Variant	Effect	Δscore
15:75260368:CACA:C	acceptor_loss	1.0000
15:75260369:ACAG:A	acceptor_loss	1.0000
15:75260370:C:G	acceptor_gain	1.0000
15:75260371:A:AG	acceptor_gain	1.0000
15:75260371:AG:A	acceptor_loss	1.0000
15:75260372:G:GA	acceptor_gain	1.0000
15:75260372:GC:G	acceptor_gain	1.0000
15:75260372:GCT:G	acceptor_gain	1.0000
15:75260372:GCTA:G	acceptor_gain	1.0000
15:75260372:GCTAA:G	acceptor_gain	1.0000
15:75260471:T:TA	donor_gain	1.0000
15:75260472:G:GA	donor_gain	1.0000
15:75260488:GGGAT:G	donor_gain	1.0000
15:75260489:GGAT:G	donor_gain	1.0000
15:75260489:GGATG:G	donor_gain	1.0000
15:75260490:G:T	donor_gain	1.0000
15:75260490:GAT:G	donor_gain	1.0000
15:75260490:GATG:G	donor_gain	1.0000
15:75260493:G:GG	donor_gain	1.0000
15:75262372:A:AG	acceptor_gain	1.0000
15:75262373:C:G	acceptor_gain	1.0000
15:75262374:A:AG	acceptor_gain	1.0000
15:75262385:A:AG	acceptor_gain	1.0000
15:75262386:A:G	acceptor_gain	1.0000
15:75262402:T:G	acceptor_gain	1.0000
15:75263384:G:GT	donor_gain	1.0000
15:75263387:G:GG	donor_gain	1.0000
15:75263976:GAA:G	acceptor_gain	1.0000
15:75263976:GAAGA:G	acceptor_gain	1.0000
15:75264072:G:GT	donor_gain	1.0000

AlphaMissense

4557 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:75263812:T:C	L130P	0.915
15:75263833:T:C	L137S	0.897
15:75263874:T:C	F151L	0.890
15:75263876:C:A	F151L	0.890
15:75263876:C:G	F151L	0.890
15:75265394:G:C	W243C	0.883
15:75265394:G:T	W243C	0.883
15:75265392:T:A	W243R	0.881
15:75265392:T:C	W243R	0.881
15:75263982:T:C	S155P	0.876
15:75266177:T:C	L307P	0.875
15:75265351:G:C	R229P	0.868
15:75265669:T:C	L271P	0.868
15:75266210:T:C	L318P	0.850
15:75263826:G:C	A135P	0.849
15:75263865:G:C	A148P	0.845
15:75263845:T:C	L141P	0.844
15:75266167:G:C	A304P	0.833
15:75262470:T:C	L88P	0.826
15:75263869:G:C	R149P	0.818
15:75263862:G:C	A147P	0.813
15:75264004:T:C	L162P	0.808
15:75265393:G:C	W243S	0.805
15:75263648:G:C	A109P	0.800
15:75265330:T:C	L222P	0.794
15:75269459:T:C	F534L	0.793
15:75269461:T:A	F534L	0.793
15:75269461:T:G	F534L	0.793
15:75263821:A:T	E133V	0.782
15:75269898:T:C	F623L	0.780

dbSNP variants (sampled 300 via entrez): RS1001087426 (15:75273537 G>A,C,T), RS1002057812 (15:75265154 G>A), RS1002495489 (15:75263582 G>A), RS1004053497 (15:75269526 T>C), RS1005059063 (15:75258286 AT>A), RS1007944056 (15:75270309 C>A,G,T), RS1008137656 (15:75269832 G>A,T), RS1008951320 (15:75260317 G>A,T), RS1009736126 (15:75273357 A>G), RS1009768571 (15:75270947 T>C), RS1010726094 (15:75263504 T>C), RS1010755581 (15:75260339 T>A,G), RS1015279167 (15:75263877 G>A), RS1019376094 (15:75270326 T>C), RS1021168739 (15:75273478 G>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
GCST004749_41	Lung cancer in ever smokers	6.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation	1
Cadmium Chloride	decreases expression	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

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