GOLGA6D

Summary

GOLGA6D (golgin A6 family member D, HGNC:32204) is a protein-coding gene on chromosome 15q24.2, encoding Golgin subfamily A member 6D (P0CG33). It is a selective cancer dependency (DepMap: 22.4% of cell lines).

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 653643 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 89 total
• Cancer dependency (DepMap): dependent in 22.4% of screened cell lines
• MANE Select transcript: NM_001145224

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32204
Approved symbol	GOLGA6D
Name	golgin A6 family member D
Location	15q24.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000140478
Ensembl biotype	protein_coding
Entrez	653643

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000434739

RefSeq mRNA: 1 — MANE Select: NM_001145224 NM_001145224

CCDS: CCDS45308

Canonical transcript exons

ENST00000434739 — 18 exons

Exon	Start	End
ENSE00001762458	75294348	75295530
ENSE00002435111	75287629	75287667
ENSE00002436093	75289592	75289699
ENSE00002448664	75292565	75292640
ENSE00002449876	75291166	75291234
ENSE00002452268	75289892	75289979
ENSE00002459521	75287929	75287979
ENSE00002469562	75293915	75294018
ENSE00002473647	75284650	75284769
ENSE00002477542	75286693	75286773
ENSE00002480645	75289397	75289483
ENSE00002482271	75290381	75290889
ENSE00002492439	75288258	75288364
ENSE00002507280	75294108	75294261
ENSE00002509064	75293073	75293164
ENSE00002521332	75293729	75293831
ENSE00002531442	75288080	75288161
ENSE00002610606	75282835	75282959

Expression profiles

Bgee: expression breadth broad, 43 present calls, max score 86.91.

Top tissues by expression

74 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	86.91	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.79	gold quality
right testis	UBERON:0004534	76.79	gold quality
testis	UBERON:0000473	76.51	gold quality
left testis	UBERON:0004533	76.48	gold quality
liver	UBERON:0002107	60.75	gold quality
right lobe of liver	UBERON:0001114	56.84	gold quality
skeletal muscle tissue	UBERON:0001134	51.63	gold quality
cerebellum	UBERON:0002037	49.72	gold quality
cerebellar cortex	UBERON:0002129	49.68	gold quality
cerebellar hemisphere	UBERON:0002245	49.40	gold quality
right coronary artery	UBERON:0001625	49.31	gold quality
sural nerve	UBERON:0015488	48.97	gold quality
apex of heart	UBERON:0002098	48.23	gold quality
right hemisphere of cerebellum	UBERON:0014890	48.07	gold quality
muscle of leg	UBERON:0001383	47.83	gold quality
bone marrow cell	CL:0002092	47.02	gold quality
gastrocnemius	UBERON:0001388	46.78	gold quality
muscle tissue	UBERON:0002385	45.75	gold quality
right uterine tube	UBERON:0001302	44.05	silver quality
tibial artery	UBERON:0007610	43.94	gold quality
popliteal artery	UBERON:0002250	43.87	gold quality
colonic epithelium	UBERON:0000397	41.23	gold quality
ventricular zone	UBERON:0003053	40.63	gold quality
endometrium	UBERON:0001295	40.57	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	40.49	silver quality
bone marrow	UBERON:0002371	40.47	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	39.99	silver quality
calcaneal tendon	UBERON:0003701	39.84	gold quality
tibial nerve	UBERON:0001323	39.23	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

61 targeting GOLGA6D, 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-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
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-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-202-5P	99.78	67.65	991
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-1287-3P	99.63	66.93	492
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

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 22.4% 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): GOLGA8F (ENSG00000153684), GOLGA6A (ENSG00000159289), 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 6D — P0CG33 (reviewed: P0CG33)

All UniProt accessions (1): P0CG33

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the GOLGA6 family.

RefSeq proteins (1): NP_001138696* (*=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-P0CG33-F1	74.46	0.50

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 23 (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, MIR4719, MIR3143, MIR4672, MIR2113, MIR10522_5P

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

118 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GOLGA6D	ITSN2	Q9NZM3	238
GOLGA6D	RPL29	P47914	161
GOLGA6D	BTBD18	B2RXH4	161
GOLGA6D	DDX6	P26196	161
GOLGA6D	SHC1	P29353	160
GOLGA6D	GOLGA7	Q7Z5G4	154
GOLGA6D	ITSN1	Q15811	151
GOLGA6D	USO1	O60763	132
GOLGA6D	TRIP11	Q15643	132
GOLGA6D	GORASP2	Q9H8Y8	128
GOLGA6D	GORASP1	Q9BQQ3	128
GOLGA6D	STX5	Q13190	115
GOLGA6D	GOLGB1	Q14789	114
GOLGA6D	VPS35	Q96QK1	109
GOLGA6D	GOSR1	O95249	106

IntAct

2 interactions, top by confidence:

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

BioGRID (2): 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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	74
Likely benign	15
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2847 predictions. Top by Δscore:

Variant	Effect	Δscore
15:75284645:CACA:C	acceptor_loss	1.0000
15:75284647:CA:C	acceptor_loss	1.0000
15:75284648:A:AG	acceptor_gain	1.0000
15:75284648:AGC:A	acceptor_loss	1.0000
15:75284649:G:GA	acceptor_gain	1.0000
15:75284649:G:GT	acceptor_loss	1.0000
15:75284649:GCT:G	acceptor_gain	1.0000
15:75284649:GCTA:G	acceptor_gain	1.0000
15:75284748:T:TA	donor_gain	1.0000
15:75284749:G:GA	donor_gain	1.0000
15:75284765:GGGAT:G	donor_gain	1.0000
15:75284766:GGAT:G	donor_gain	1.0000
15:75284766:GGATG:G	donor_gain	1.0000
15:75284767:G:GT	donor_gain	1.0000
15:75284767:G:T	donor_gain	1.0000
15:75284767:GAT:G	donor_gain	1.0000
15:75284770:G:GG	donor_gain	1.0000
15:75286653:A:AG	acceptor_gain	1.0000
15:75286654:C:G	acceptor_gain	1.0000
15:75286655:A:AG	acceptor_gain	1.0000
15:75286666:A:AG	acceptor_gain	1.0000
15:75286667:A:G	acceptor_gain	1.0000
15:75286683:T:G	acceptor_gain	1.0000
15:75287665:G:GT	donor_gain	1.0000
15:75287668:G:GG	donor_gain	1.0000
15:75288353:G:GT	donor_gain	1.0000
15:75288361:CAGGG:C	donor_loss	1.0000
15:75288362:AGGG:A	donor_loss	1.0000
15:75288363:GG:G	donor_gain	1.0000
15:75288364:GG:G	donor_gain	1.0000

AlphaMissense

4557 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:75288093:T:C	L130P	0.944
15:75288114:T:C	L137S	0.919
15:75289944:T:C	L271P	0.903
15:75288107:G:C	A135P	0.901
15:75290453:T:C	L307P	0.897
15:75290486:T:C	L318P	0.891
15:75286751:T:C	L88P	0.883
15:75288155:T:C	F151L	0.883
15:75288157:C:A	F151L	0.883
15:75288157:C:G	F151L	0.883
15:75287929:G:C	A109P	0.875
15:75289626:G:C	R229P	0.871
15:75289669:G:C	W243C	0.871
15:75289669:G:T	W243C	0.871
15:75289667:T:A	W243R	0.868
15:75289667:T:C	W243R	0.868
15:75290443:G:C	A304P	0.858
15:75288263:T:C	S155P	0.850
15:75288102:A:T	E133V	0.834
15:75294174:T:C	F623L	0.818
15:75294176:C:A	F623L	0.818
15:75294176:C:G	F623L	0.818
15:75288103:A:C	E133D	0.810
15:75288103:A:T	E133D	0.810
15:75289605:T:C	L222P	0.806
15:75288093:T:A	L130H	0.795
15:75287660:T:C	L106P	0.784
15:75289668:G:C	W243S	0.784
15:75288146:G:C	A148P	0.783
15:75289637:G:C	A233P	0.782

dbSNP variants (sampled 300 via entrez): RS1001455142 (15:75275621 G>A), RS1002855553 (15:75295910 C>T), RS1002886623 (15:75295672 C>CT), RS1002918073 (15:75275812 A>C), RS1004710568 (15:75295945 C>A), RS1005928488 (15:75294129 G>A,C), RS1006128424 (15:75293661 G>A), RS1006718049 (15:75280665 G>A), RS1007348038 (15:75286163 T>C), RS1011570887 (15:75295623 G>A,C,T), RS1012206138 (15:75295882 A>C,G), RS1012533824 (15:75289499 G>A), RS1013535190 (15:75275679 T>G), RS1013754531 (15:75279043 T>A,C), RS1016476271 (15:75295965 A>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

1 associations (top):

Study	Trait	p-value
GCST007725_8	Serum uric acid levels	1.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004761	uric acid measurement

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
bisphenol A	increases expression	1
Benzo(a)pyrene	increases methylation	1

Clinical trials (associated diseases)

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