GSG1

Summary

GSG1 (germ cell associated 1, HGNC:19716) is a protein-coding gene on chromosome 12p13.1, encoding Germ cell-specific gene 1 protein (Q2KHT4). May cause the redistribution of PAPOLB from the cytosol to the endoplasmic reticulum.

Predicted to enable RNA polymerase binding activity. Predicted to be located in endoplasmic reticulum membrane. Predicted to be active in plasma membrane.

Source: NCBI Gene 83445 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 69 total
• MANE Select transcript: NM_001080555

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19716
Approved symbol	GSG1
Name	germ cell associated 1
Location	12p13.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC3146
Ensembl gene	ENSG00000111305
Ensembl biotype	protein_coding
Entrez	83445

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 10 protein_coding

ENST00000337630, ENST00000351606, ENST00000396302, ENST00000432710, ENST00000457134, ENST00000537302, ENST00000542415, ENST00000545401, ENST00000545699, ENST00000651961

RefSeq mRNA: 15 — MANE Select: NM_001080555 NM_001080554, NM_001080555, NM_001206842, NM_001206843, NM_001206845, NM_001367358, NM_001367359, NM_001367360, NM_001367361, NM_001367362, NM_001367363, NM_001367364, NM_001368007, NM_031289, NM_153823

CCDS: CCDS44835, CCDS44836, CCDS55806, CCDS55807, CCDS55808, CCDS8659, CCDS91657

Canonical transcript exons

ENST00000651961 — 7 exons

Exon	Start	End
ENSE00001095868	13089208	13089276
ENSE00001299582	13088862	13088909
ENSE00001683055	13103465	13103667
ENSE00001839096	13083532	13085243
ENSE00003471732	13090503	13090818
ENSE00003520474	13087152	13087263
ENSE00003674036	13087907	13088059

Expression profiles

Bgee: expression breadth ubiquitous, 143 present calls, max score 98.82.

FANTOM5 (CAGE): breadth broad, TPM avg 2.9408 / max 1109.2139, expressed in 207 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
129780	1.0729	87
129786	0.6848	41
129779	0.5952	61
129787	0.4780	7
129781	0.0538	6
129785	0.0340	17
129782	0.0221	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	98.82	gold quality
right testis	UBERON:0004534	98.67	gold quality
sperm	CL:0000019	98.45	gold quality
male germ cell	CL:0000015	96.43	gold quality
adult organism	UBERON:0007023	96.00	gold quality
testis	UBERON:0000473	95.39	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.00	gold quality
body of pancreas	UBERON:0001150	69.95	gold quality
pancreas	UBERON:0001264	62.02	gold quality
prefrontal cortex	UBERON:0000451	61.59	gold quality
stromal cell of endometrium	CL:0002255	60.55	gold quality
anterior cingulate cortex	UBERON:0009835	57.35	gold quality
cingulate cortex	UBERON:0003027	57.33	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	56.96	gold quality
jejunal mucosa	UBERON:0000399	56.40	gold quality
metanephros cortex	UBERON:0010533	56.38	gold quality
frontal cortex	UBERON:0001870	55.72	gold quality
neocortex	UBERON:0001950	55.54	gold quality
cortical plate	UBERON:0005343	55.45	gold quality
Brodmann (1909) area 9	UBERON:0013540	55.25	gold quality
choroid plexus epithelium	UBERON:0003911	55.15	silver quality
right frontal lobe	UBERON:0002810	54.93	gold quality
cerebral cortex	UBERON:0000956	53.40	gold quality
duodenum	UBERON:0002114	52.29	gold quality
metanephros	UBERON:0000081	52.07	gold quality
cortex of kidney	UBERON:0001225	51.54	gold quality
telencephalon	UBERON:0001893	51.37	gold quality
hypothalamus	UBERON:0001898	50.70	gold quality
forebrain	UBERON:0001890	50.22	gold quality
nucleus accumbens	UBERON:0001882	50.16	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	1278.68
E-MTAB-11121	yes	624.95
E-GEOD-134144	yes	32.98
E-MTAB-7249	no	15.29
E-ANND-3	no	3.40

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ESR1

miRNA regulators (miRDB)

77 targeting GSG1, 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-1252-5P	100.00	69.80	2774
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-371A-3P	99.99	66.77	91
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-34B-5P	99.78	67.56	1175
HSA-MIR-449C-5P	99.78	67.63	1168
HSA-MIR-2682-5P	99.73	67.38	1055
HSA-MIR-5580-3P	99.70	69.41	2052
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-545-5P	99.66	70.18	2308
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-4524A-5P	99.57	71.73	1193
HSA-MIR-4524B-5P	99.57	71.68	1195
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-889-5P	99.41	68.75	1025
HSA-MIR-7515	99.31	68.22	1795
HSA-MIR-148A-5P	99.30	68.27	1141
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gsg1	ENSMUSG00000030206
rattus_norvegicus	Gsg1	ENSRNOG00000008518

Paralogs (10): LIM2 (ENSG00000105370), NKG7 (ENSG00000105374), PMP22 (ENSG00000109099), EMP1 (ENSG00000134531), EMP3 (ENSG00000142227), CLDND2 (ENSG00000160318), GSG1L (ENSG00000169181), TMEM202 (ENSG00000187806), EMP2 (ENSG00000213853), GSG1L2 (ENSG00000214978)

Protein

Protein identifiers

Germ cell-specific gene 1 protein — Q2KHT4 (reviewed: Q2KHT4)

All UniProt accessions (8): A0A494C0G6, Q2KHT4, F1T0A0, F1T0A1, F5GYH0, F5H0V9, F5H134, G3XAB9

UniProt curated annotations — full annotation on UniProt →

Function. May cause the redistribution of PAPOLB from the cytosol to the endoplasmic reticulum.

Subunit / interactions. Interacts with PAPOLB.

Subcellular location. Endoplasmic reticulum membrane.

Similarity. Belongs to the GSG1 family.

Isoforms (8)

UniProt ID	Names	Canonical?
Q2KHT4-1	1	yes
Q2KHT4-2	2
Q2KHT4-3	3
Q2KHT4-4	4
Q2KHT4-5	5
Q2KHT4-6	6
Q2KHT4-7	7
Q2KHT4-8	8

RefSeq proteins (15): NP_001074023, NP_001074024, NP_001193771, NP_001193772, NP_001193774, NP_001354287, NP_001354288, NP_001354289, NP_001354290, NP_001354291, NP_001354292, NP_001354293, NP_001354936, NP_112579, NP_722545 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR012478	GSG-1	Family
IPR050579	PMP-22/EMP/MP20-like	Family

Pfam: PF07803

UniProt features (15 total): splice variant 6, transmembrane region 4, sequence variant 2, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q2KHT4-F1	70.79	0.35

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 77 (showing top): LI_CISPLATIN_RESISTANCE_DN, KORKOLA_CHORIOCARCINOMA_DN, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, KORKOLA_EMBRYONAL_CARCINOMA_DN, GNF2_CCNA1, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, SENESE_HDAC3_TARGETS_DN, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_ORGANELLE_SUBCOMPARTMENT, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_36HR, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D, ATF2_S_UP.V1_UP, PRC2_EED_DN.V1_UP, ALK_DN.V1_DN, KRAS.BREAST_UP.V1_UP

GO Biological Process (0):

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

GO Cellular Component (4): endoplasmic reticulum membrane (GO:0005789), plasma membrane (GO:0005886), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
membrane	1
cell periphery	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

354 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GSG1	RIMKLB	Q9ULI2	491
GSG1	SCAPER	Q9BY12	477
GSG1	TMEM39B	Q9GZU3	392
GSG1	OR6A2	O95222	369
GSG1	CASKIN2	Q8WXE0	348
GSG1	VWC2	Q2TAL6	335
GSG1	PRRT1	Q99946	330
GSG1	PPP2R5B	Q15173	317
GSG1	SLF2	Q8IX21	316
GSG1	SH3BGR	P55822	300
GSG1	RHEBL1	Q8TAI7	288
GSG1	FAM124B	Q9H5Z6	288
GSG1	NRN1	Q9NPD7	284
GSG1	SIGLEC11	Q96RL6	282
GSG1	TSSK2	Q96PF2	281

IntAct

5 interactions, top by confidence:

A	B	Type	Score
TRAF2	GSG1	psi-mi:“MI:0915”(physical association)	0.560
GSG1	TRAF2	psi-mi:“MI:0915”(physical association)	0.560
GSG1	IL37	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (14): GSG1 (Two-hybrid), ASAH1 (Affinity Capture-MS), IL37 (Affinity Capture-MS), IL37 (Affinity Capture-MS), ASAH1 (Affinity Capture-MS), GSG1 (Two-hybrid), ARFIP2 (Two-hybrid), FTHL17 (Two-hybrid), SDCBP (Two-hybrid), SYT16 (Two-hybrid), PITPNC1 (Two-hybrid), MIEF2 (Two-hybrid), IL37 (Affinity Capture-MS), GSG1 (Protein-peptide)

ESM2 similar proteins: A0A494BZU4, A0A7H0DND7, A0JNG0, A2T345, A4IIV4, C4QM85, E7F594, G5EDX4, O02051, O45306, P0DP42, P0DST5, P0DST6, P21061, P24763, P34362, P34363, P53053, Q09282, Q0II41, Q10907, Q11071, Q11085, Q13571, Q20249, Q297K8, Q2KHT4, Q2KJA5, Q32KQ5, Q5DC12, Q5GH77, Q5PQM0, Q5RD28, Q5REZ0, Q5TAH2, Q61168, Q6AXT9, Q6GV27, Q6GV28, Q7K1V5

Diamond homologs: A4IIV4, A8MUP6, D3Z7H4, D3ZK93, Q2KHT4, Q3SZT1, Q4V922, Q6AYL2, Q6UXU4, Q8R1W2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	13
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1002 predictions. Top by Δscore:

Variant	Effect	Δscore
12:13085239:CCATG:C	acceptor_gain	1.0000
12:13085240:CATG:C	acceptor_gain	1.0000
12:13085240:CATGC:C	acceptor_gain	1.0000
12:13085242:TG:T	acceptor_gain	1.0000
12:13085244:C:CC	acceptor_gain	1.0000
12:13087150:A:AC	donor_gain	1.0000
12:13087151:C:CC	donor_gain	1.0000
12:13088794:C:A	donor_gain	1.0000
12:13085241:ATG:A	acceptor_gain	0.9900
12:13085243:GCTA:G	acceptor_loss	0.9900
12:13085244:C:CA	acceptor_loss	0.9900
12:13085245:T:C	acceptor_loss	0.9900
12:13085254:A:AC	acceptor_gain	0.9900
12:13085254:A:C	acceptor_gain	0.9900
12:13087151:CT:C	donor_gain	0.9900
12:13087151:CTA:C	donor_gain	0.9900
12:13087151:CTAGA:C	donor_gain	0.9900
12:13087261:GACCT:G	acceptor_loss	0.9900
12:13087263:CCTAC:C	acceptor_loss	0.9900
12:13087264:CTACC:C	acceptor_loss	0.9900
12:13087265:T:A	acceptor_loss	0.9900
12:13087900:AACTC:A	donor_loss	0.9900
12:13087901:ACTCA:A	donor_loss	0.9900
12:13087902:CTCA:C	donor_loss	0.9900
12:13087903:TCAC:T	donor_loss	0.9900
12:13087904:CA:C	donor_loss	0.9900
12:13087905:A:C	donor_loss	0.9900
12:13087906:C:CG	donor_loss	0.9900
12:13088060:C:CC	acceptor_gain	0.9900
12:13088064:C:CT	acceptor_gain	0.9900

AlphaMissense

2366 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000063842 (12:13085984 C>G), RS1000869738 (12:13105310 A>G), RS1001014209 (12:13098521 A>C), RS1001142420 (12:13102045 G>C), RS1001225470 (12:13083928 CT>C), RS1001469319 (12:13102846 T>A), RS1001477195 (12:13102492 A>G), RS1001508746 (12:13098866 T>G), RS1001564253 (12:13102260 A>G), RS1002110345 (12:13097407 C>T), RS1002163892 (12:13090699 C>T), RS1002173096 (12:13096248 C>T), RS1002418698 (12:13097221 T>C), RS1002470662 (12:13100219 G>A,T), RS1002567089 (12:13100493 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
GCST005988_10	Serum albumin levels	1.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	2
Aflatoxin B1	decreases methylation, increases methylation	2
butyraldehyde	increases expression	1
fipronil	affects cotreatment, decreases expression	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	increases expression	1
jinfukang	decreases expression	1
incobotulinumtoxinA	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	decreases expression	1
Copper	affects cotreatment, decreases expression	1
DEET	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	increases expression	1
Valproic Acid	decreases methylation	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Copper Sulfate	increases expression	1
Particulate Matter	decreases expression	1

Clinical trials (associated diseases)

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