GINM1

Summary

GINM1 (glycosylated integral membrane protein 1, HGNC:21074) is a protein-coding gene on chromosome 6q25.1, encoding Glycoprotein integral membrane protein 1 (Q9NU53).

Predicted to be located in membrane.

Source: NCBI Gene 116254 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 60 total — 2 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_138785

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21074
Approved symbol	GINM1
Name	glycosylated integral membrane protein 1
Location	6q25.1
Locus type	gene with protein product
Status	Approved
Aliases	dJ12G14.2
Ensembl gene	ENSG00000055211
Ensembl biotype	protein_coding
Entrez	116254

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 9 protein_coding, 1 nonsense_mediated_decay

ENST00000367419, ENST00000433539, ENST00000650599, ENST00000902972, ENST00000902973, ENST00000902974, ENST00000902975, ENST00000902976, ENST00000902977, ENST00000920354

RefSeq mRNA: 1 — MANE Select: NM_138785 NM_138785

CCDS: CCDS5216

Canonical transcript exons

ENST00000367419 — 8 exons

Exon	Start	End
ENSE00000439992	149582440	149582603
ENSE00000765080	149580593	149580723
ENSE00000765081	149579834	149579990
ENSE00001701692	149590727	149591748
ENSE00002435363	149578822	149578973
ENSE00002466164	149572285	149572344
ENSE00002525098	149572507	149572603
ENSE00003842008	149566375	149566534

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 99.34.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.7950 / max 204.3812, expressed in 1821 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
70491	16.3950	1808
70492	13.1110	1790
70489	5.0543	1516
70490	0.2347	77

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	99.34	gold quality
sperm	CL:0000019	97.57	gold quality
decidua	UBERON:0002450	96.86	gold quality
renal medulla	UBERON:0000362	96.75	gold quality
descending thoracic aorta	UBERON:0002345	96.25	gold quality
smooth muscle tissue	UBERON:0001135	96.02	gold quality
mammary duct	UBERON:0001765	95.95	gold quality
epithelium of mammary gland	UBERON:0003244	95.94	gold quality
pericardium	UBERON:0002407	95.92	gold quality
vena cava	UBERON:0004087	95.89	gold quality
right coronary artery	UBERON:0001625	95.85	gold quality
calcaneal tendon	UBERON:0003701	95.79	gold quality
mucosa of stomach	UBERON:0001199	95.76	gold quality
thoracic aorta	UBERON:0001515	95.61	gold quality
tibial artery	UBERON:0007610	95.61	gold quality
popliteal artery	UBERON:0002250	95.60	gold quality
aorta	UBERON:0000947	95.58	gold quality
ascending aorta	UBERON:0001496	95.54	gold quality
layer of synovial tissue	UBERON:0007616	95.41	gold quality
left coronary artery	UBERON:0001626	95.02	gold quality
saphenous vein	UBERON:0007318	95.02	gold quality
tendon	UBERON:0000043	95.01	gold quality
coronary artery	UBERON:0001621	94.83	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.83	gold quality
nipple	UBERON:0002030	94.82	gold quality
urethra	UBERON:0000057	94.80	gold quality
endocervix	UBERON:0000458	94.76	gold quality
spinal cord	UBERON:0002240	94.68	gold quality
adult mammalian kidney	UBERON:0000082	94.60	gold quality
corpus epididymis	UBERON:0004359	94.44	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-6678	yes	4.12
E-HCAD-5	no	2.17
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ginm1	ENSDARG00000021975
mus_musculus	Ginm1	ENSMUSG00000040006
rattus_norvegicus	Ginm1	ENSRNOG00000015239

Protein

Protein identifiers

Glycoprotein integral membrane protein 1 — Q9NU53 (reviewed: Q9NU53)

All UniProt accessions (3): A0A3B3IRL9, Q9NU53, Q5TFA5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_620140* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR042319	GINM1	Family

UniProt features (9 total): glycosylation site 4, topological domain 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NU53-F1	70.88	0.45

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (4): 46, 64, 166, 191

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 83 (showing top): chr6q25, MARTINEZ_RB1_TARGETS_DN, AACTTT_UNKNOWN, CUI_TCF21_TARGETS_2_DN, BURTON_ADIPOGENESIS_5, MARTINEZ_RB1_AND_TP53_TARGETS_UP, GEORGES_TARGETS_OF_MIR192_AND_MIR215, GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, FEVR_CTNNB1_TARGETS_UP, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_WITH_H4K20ME1_MARK, GSE14415_INDUCED_TREG_VS_FOXP3_KO_INDUCED_TREG_DN, GSE5503_PLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, GSE13547_CTRL_VS_ANTI_IGM_STIM_ZFX_KO_BCELL_2H_DN

GO Biological Process (0):

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

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

308 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GINM1	LCTL	Q6UWM7	572
GINM1	S100A5	P33763	522
GINM1	JRKL	Q9Y4A0	508
GINM1	PIP4K2C	Q8TBX8	504
GINM1	UBE2G1	P62253	504
GINM1	S100A14	Q9HCY8	489
GINM1	KRTAP11-1	Q8IUC1	446
GINM1	HBS1L	Q9Y450	443
GINM1	PAQR5	Q9NXK6	439
GINM1	ILF2	Q12905	438
GINM1	GPR153	Q6NV75	436
GINM1	OPHN1	O60890	432
GINM1	TUT4	Q5TAX3	428
GINM1	USP11	P51784	423
GINM1	GLOD4	Q9HC38	412

IntAct

28 interactions, top by confidence:

A	B	Type	Score
FATE1	GINM1	psi-mi:“MI:0915”(physical association)	0.560
ITGB8	GET1	psi-mi:“MI:0914”(association)	0.530
GINM1	ADCY9	psi-mi:“MI:0914”(association)	0.530
GINM1	CFTR	psi-mi:“MI:0915”(physical association)	0.370
MPPE1	ADAM10	psi-mi:“MI:0914”(association)	0.350
PCDHGA5	MAP2K7	psi-mi:“MI:0914”(association)	0.350
GINM1	TNFRSF10B	psi-mi:“MI:0914”(association)	0.350
HS3ST2	HSPA5	psi-mi:“MI:0914”(association)	0.350
EPO	EPOR	psi-mi:“MI:0914”(association)	0.350
NS3	C15orf61	psi-mi:“MI:0914”(association)	0.350
	TMEM223	psi-mi:“MI:0914”(association)	0.350
GINM1	FAM234B	psi-mi:“MI:0914”(association)	0.350
MPPE1	FAM234B	psi-mi:“MI:0914”(association)	0.350
SMIM5	KLRG2	psi-mi:“MI:0914”(association)	0.350
CSTL1	DENND11	psi-mi:“MI:0914”(association)	0.350
KIR2DL4	GPR89A	psi-mi:“MI:0914”(association)	0.350
TMPRSS13	TOR1A	psi-mi:“MI:0914”(association)	0.350
PCDHGA5	AREL1	psi-mi:“MI:0914”(association)	0.350
CTXN1	ABCC4	psi-mi:“MI:0914”(association)	0.350
HS3ST2	PIGA	psi-mi:“MI:0914”(association)	0.350
GINM1	KDELR1	psi-mi:“MI:0914”(association)	0.350
SLC17A9	PIPSL	psi-mi:“MI:0914”(association)	0.350
TMEM241	FAAH	psi-mi:“MI:0914”(association)	0.350
GINM1	FATE1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (169): B4GALT7 (Affinity Capture-MS), KIAA1467 (Affinity Capture-MS), KIAA0319L (Affinity Capture-MS), CSGALNACT2 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), NDFIP1 (Affinity Capture-MS), TFIP11 (Affinity Capture-MS), HLA-F (Affinity Capture-MS), TMX2 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS), PLEKHA5 (Affinity Capture-MS), GLCE (Affinity Capture-MS), CALCB (Affinity Capture-MS), PDZD11 (Affinity Capture-MS)

ESM2 similar proteins: A0A096P2H6, A0A0D9S1R4, A2APA5, A9CBA0, P06740, P06759, P0DKU6, P0DKW1, P0DKW2, P0DKW3, P0DKW4, P0DKY3, P0DML4, P0DML5, P0DML6, P0DMN8, P0DOC4, P0DP53, P0DTG9, P0DTH0, P0DTH1, P0DTH2, P0DTH3, P0DTH4, P0DUP5, P0DUP6, P22749, P33622, P35225, P55056, P55057, P55797, Q0VCT2, Q13790, Q3SYR5, Q3ZRW9, Q5HZE8, Q5JTB6, Q5JX69, Q5JX71

Diamond homologs: Q5RBQ2, Q5RII3, Q91WR6, Q9NU53

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	1
Uncertain significance	37
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
146082	GRCh38/hg38 6q24.3-25.1(chr6:147805119-150893715)x1	Pathogenic
147845	GRCh38/hg38 6q24.3-25.1(chr6:148112335-149649984)x1	Pathogenic
442634	GRCh37/hg19 6q24.3-25.1(chr6:148364229-149928368)x1	Likely pathogenic

SpliceAI

1130 predictions. Top by Δscore:

Variant	Effect	Δscore
6:149566530:CACAG:C	donor_loss	1.0000
6:149566531:ACAGG:A	donor_loss	1.0000
6:149566533:AGGTA:A	donor_loss	1.0000
6:149566534:GG:G	donor_loss	1.0000
6:149566535:GT:G	donor_loss	1.0000
6:149566536:T:G	donor_loss	1.0000
6:149578974:G:GG	donor_gain	1.0000
6:149579829:CACA:C	acceptor_loss	1.0000
6:149579831:CA:C	acceptor_loss	1.0000
6:149579832:A:G	acceptor_loss	1.0000
6:149579991:G:C	donor_loss	1.0000
6:149579992:T:A	donor_loss	1.0000
6:149580587:G:A	acceptor_gain	1.0000
6:149580592:GAAA:G	acceptor_gain	1.0000
6:149582601:CAA:C	donor_gain	1.0000
6:149582602:AA:A	donor_gain	1.0000
6:149582604:G:GG	donor_gain	1.0000
6:149590725:A:AG	acceptor_gain	1.0000
6:149590725:AGAG:A	acceptor_gain	1.0000
6:149590726:G:GG	acceptor_gain	1.0000
6:149590726:GA:G	acceptor_gain	1.0000
6:149590726:GAGG:G	acceptor_gain	1.0000
6:149590726:GAGGA:G	acceptor_gain	1.0000
6:149572277:TTTTA:T	acceptor_loss	0.9900
6:149572278:TTTAC:T	acceptor_loss	0.9900
6:149572279:TTACA:T	acceptor_loss	0.9900
6:149572280:TACAG:T	acceptor_loss	0.9900
6:149572281:ACAG:A	acceptor_loss	0.9900
6:149572282:C:G	acceptor_loss	0.9900
6:149572283:A:AG	acceptor_gain	0.9900

AlphaMissense

2156 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:149579924:A:C	S174R	0.992
6:149579926:C:A	S174R	0.992
6:149579926:C:G	S174R	0.992
6:149572514:T:C	L63P	0.988
6:149578942:A:C	Q133P	0.982
6:149578930:T:C	L129P	0.981
6:149572508:T:A	V61D	0.976
6:149572551:T:A	N75K	0.974
6:149572551:T:G	N75K	0.974
6:149578883:G:C	R113S	0.974
6:149578883:G:T	R113S	0.974
6:149582539:G:A	G273R	0.972
6:149582539:G:C	G273R	0.972
6:149580680:T:C	L225S	0.968
6:149582548:G:A	G276R	0.967
6:149582548:G:C	G276R	0.967
6:149579931:T:A	L176H	0.966
6:149582446:T:C	C242R	0.963
6:149572550:A:T	N75I	0.960
6:149582446:T:A	C242S	0.959
6:149582447:G:C	C242S	0.959
6:149572580:G:C	R85P	0.957
6:149578882:G:C	R113T	0.956
6:149578901:G:C	W119C	0.956
6:149578901:G:T	W119C	0.956
6:149582540:G:A	G273E	0.956
6:149572547:T:A	V74E	0.952
6:149578882:G:T	R113M	0.952
6:149579954:G:C	D184H	0.952
6:149582549:G:A	G276E	0.952

dbSNP variants (sampled 300 via entrez): RS1000040656 (6:149585839 G>A), RS1000130949 (6:149573149 C>G), RS1000178859 (6:149567779 C>T), RS1000284535 (6:149592081 A>G), RS1000417578 (6:149579955 A>T), RS1000466032 (6:149574211 C>T), RS1000598115 (6:149574306 C>T), RS1000741934 (6:149566769 A>G), RS1000959707 (6:149587475 G>C), RS1001087245 (6:149591802 T>A,C,G), RS1001176647 (6:149586453 A>C), RS1001181535 (6:149569285 C>G), RS1001208969 (6:149568722 T>G), RS1001344488 (6:149573402 A>G), RS1001418038 (6:149581673 T>C)

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

3 associations (top):

Study	Trait	p-value
GCST003775_6	Lung cancer	1.000000e-07
GCST010702_29	Subcortical volume (MOSTest)	7.000000e-11
GCST010703_317	Brain morphology (MOSTest)	7.000000e-22

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression	3
Air Pollutants	decreases expression, increases abundance	2
Cisplatin	decreases expression, increases expression	2
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
entinostat	increases expression	1
K 7174	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
jinfukang	decreases expression	1
Acetaminophen	increases expression	1
Catechin	affects cotreatment, increases expression	1
Diuron	decreases expression	1
Smoke	decreases expression, increases abundance	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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