YIPF1

Summary

YIPF1 (Yip1 domain family member 1, HGNC:25231) is a protein-coding gene on chromosome 1p32.3, encoding Protein YIPF1 (Q9Y548).

Predicted to enable small GTPase binding activity. Predicted to be involved in vesicle-mediated transport. Located in several cellular components, including Golgi apparatus subcompartment; nucleoplasm; and transport vesicle.

Source: NCBI Gene 54432 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 62 total
• MANE Select transcript: NM_018982

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25231
Approved symbol	YIPF1
Name	Yip1 domain family member 1
Location	1p32.3
Locus type	gene with protein product
Status	Approved
Aliases	DJ167A19.1, FinGER1, Yip5a, YIPFbeta3A
Ensembl gene	ENSG00000058799
Ensembl biotype	protein_coding
OMIM	617521
Entrez	54432

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 10 protein_coding, 4 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000072644, ENST00000371399, ENST00000464950, ENST00000465897, ENST00000469457, ENST00000472983, ENST00000480151, ENST00000854787, ENST00000854788, ENST00000854789, ENST00000854790, ENST00000854791, ENST00000913540, ENST00000913541, ENST00000966545

RefSeq mRNA: 1 — MANE Select: NM_018982 NM_018982

CCDS: CCDS584

Canonical transcript exons

ENST00000072644 — 11 exons

Exon	Start	End
ENSE00000772764	53866200	53866382
ENSE00001140284	53860056	53860153
ENSE00001383304	53889244	53889463
ENSE00001455144	53851733	53852270
ENSE00001777038	53889713	53889797
ENSE00003475789	53888907	53888986
ENSE00003548572	53878315	53878402
ENSE00003609996	53866758	53866924
ENSE00003630920	53871372	53871488
ENSE00003686208	53883113	53883276
ENSE00003693644	53878642	53878722

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 92.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.2229 / max 162.8225, expressed in 1812 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12432	21.0376	1812
12431	0.1560	41
12433	0.0219	12
12434	0.0074	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
islet of Langerhans	UBERON:0000006	92.84	gold quality
right lobe of thyroid gland	UBERON:0001119	91.94	gold quality
left lobe of thyroid gland	UBERON:0001120	91.87	gold quality
blood	UBERON:0000178	91.63	gold quality
thyroid gland	UBERON:0002046	91.47	gold quality
prostate gland	UBERON:0002367	91.30	gold quality
right adrenal gland	UBERON:0001233	91.19	gold quality
minor salivary gland	UBERON:0001830	91.15	gold quality
rectum	UBERON:0001052	90.98	gold quality
left adrenal gland	UBERON:0001234	90.91	gold quality
granulocyte	CL:0000094	90.69	gold quality
right adrenal gland cortex	UBERON:0035827	90.67	gold quality
left adrenal gland cortex	UBERON:0035825	90.61	gold quality
mouth mucosa	UBERON:0003729	90.39	gold quality
saliva-secreting gland	UBERON:0001044	90.38	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	90.38	gold quality
right lobe of liver	UBERON:0001114	90.29	gold quality
leukocyte	CL:0000738	90.11	gold quality
adrenal cortex	UBERON:0001235	89.98	gold quality
monocyte	CL:0000576	89.97	gold quality
body of stomach	UBERON:0001161	89.97	gold quality
mononuclear cell	CL:0000842	89.96	gold quality
nasal cavity epithelium	UBERON:0005384	89.94	gold quality
mucosa of transverse colon	UBERON:0004991	89.90	gold quality
adrenal gland	UBERON:0002369	89.75	gold quality
adrenal tissue	UBERON:0018303	89.53	gold quality
gastrocnemius	UBERON:0001388	89.33	gold quality
oviduct epithelium	UBERON:0004804	89.28	gold quality
pancreas	UBERON:0001264	89.17	gold quality
esophagus mucosa	UBERON:0002469	88.57	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting YIPF1, 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-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-202-3P	99.84	71.41	1290
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4663	99.62	65.33	957
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-182-3P	99.57	67.57	825
HSA-MIR-186-3P	99.51	66.24	1685
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-519D-5P	99.41	69.30	2057
HSA-MIR-548B-3P	99.38	67.26	1000
HSA-MIR-4316	99.37	65.75	1360
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-361-3P	99.19	66.45	1381
HSA-MIR-6071	99.16	67.77	1780
HSA-MIR-455-3P	98.94	67.68	878
HSA-MIR-1294	98.91	69.26	1030
HSA-MIR-9986	98.91	69.28	1024
HSA-MIR-138-2-3P	98.91	68.33	1643
HSA-MIR-3074-5P	98.82	66.56	1414
HSA-MIR-7156-3P	98.25	67.66	859
HSA-MIR-1262	98.17	66.52	757
HSA-MIR-4701-3P	98.17	66.25	788
HSA-MIR-6736-5P	98.17	66.43	760
HSA-MIR-4678	97.59	68.31	902
HSA-MIR-409-5P	97.31	68.07	364
HSA-MIR-6828-3P	96.06	67.61	1155

Literature-anchored findings (GeneRIF, showing 1)

• Knockdown of YIPF1 and YIPF2, but not that of YIPF6, also reduced intracellular glycans in HT-29 cells. Thus, we confirmed that YIPF1, YIPF2, and YIPF6 play a significant role in supporting normal glycan synthesis (PMID:28286305)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	yipf1	ENSDARG00000014474
mus_musculus	Yipf1	ENSMUSG00000057375
rattus_norvegicus	Yipf1	ENSRNOG00000010512
drosophila_melanogaster	CG4645	FBGN0030435
caenorhabditis_elegans		WBGENE00021294

Paralogs (1): YIPF2 (ENSG00000130733)

Protein

Protein identifiers

Protein YIPF1 — Q9Y548 (reviewed: Q9Y548)

Alternative names: YIP1 family member 1

All UniProt accessions (1): Q9Y548

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with YIPF6; this interaction may stabilize YIPF1. May also form a ternary complex with YIPF2 and YIPF6.

Subcellular location. Golgi apparatus. cis-Golgi network membrane. trans-Golgi network membrane. Late endosome membrane.

Similarity. Belongs to the YIP1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y548-1	1	yes
Q9Y548-2	2

RefSeq proteins (1): NP_061855* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006977	Yip1_dom	Domain
IPR039765	Yip5/YIPF1/YIPF2	Family

Pfam: PF04893

UniProt features (18 total): topological domain 6, transmembrane region 5, compositionally biased region 2, chain 1, region of interest 1, glycosylation site 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y548-F1	77.85	0.56

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 (1): 297

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 132 (showing top): GOBP_VESICLE_MEDIATED_TRANSPORT, GOMF_GTPASE_BINDING, GOCC_TRANS_GOLGI_NETWORK, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GOCC_LATE_ENDOSOME_MEMBRANE, GOCC_GOLGI_STACK, GOCC_GOLGI_CISTERNA, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, SCGGAAGY_ELK1_02, GOCC_ORGANELLE_SUBCOMPARTMENT, KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_UP, PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP, GOCC_GOLGI_TRANS_CISTERNA, GOCC_GOLGI_MEDIAL_CISTERNA

GO Biological Process (1): vesicle-mediated transport (GO:0016192)

GO Molecular Function (2): small GTPase binding (GO:0031267), protein binding (GO:0005515)

GO Cellular Component (11): Golgi trans cisterna (GO:0000138), nucleoplasm (GO:0005654), Golgi apparatus (GO:0005794), Golgi medial cisterna (GO:0005797), trans-Golgi network (GO:0005802), plasma membrane (GO:0005886), transport vesicle (GO:0030133), late endosome membrane (GO:0031902), endosome (GO:0005768), endomembrane system (GO:0012505), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
endomembrane system	3
Golgi cisterna	2
cytoplasmic vesicle	2
transport	1
cellular process	1
GTPase binding	1
binding	1
nuclear lumen	1
cytoplasm	1
intracellular membrane-bounded organelle	1
Golgi apparatus subcompartment	1
membrane	1
cell periphery	1
late endosome	1
endosome membrane	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

908 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
YIPF1	FBXO32	Q969P5	946
YIPF1	TRIM63	Q969Q1	875
YIPF1	YIPF3	Q9GZM5	792
YIPF1	FBXO25	Q8TCJ0	775
YIPF1	MSTN	O14793	666
YIPF1	MYH6	P13533	639
YIPF1	YIPF4	Q9BSR8	624
YIPF1	YIPF2	Q9BWQ6	618
YIPF1	FOXO3	O43524	584
YIPF1	IGF1	P01343	571
YIPF1	RNF2	Q99496	555
YIPF1	YIPF6	Q96EC8	543
YIPF1	MYC	P01106	529
YIPF1	FOXO1	Q12778	529
YIPF1	MYOD1	P15172	507
YIPF1	AKT1	P31749	507

IntAct

106 interactions, top by confidence:

A	B	Type	Score
YIPF1	YIPF6	psi-mi:“MI:0915”(physical association)	0.840
YIPF6	YIPF1	psi-mi:“MI:0915”(physical association)	0.840
YIPF1	YIPF6	psi-mi:“MI:0914”(association)	0.840
YIPF1	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
YIPF1	TIMMDC1	psi-mi:“MI:0915”(physical association)	0.560
YIPF1	SLC7A8	psi-mi:“MI:0915”(physical association)	0.560
YIPF1	RETREG3	psi-mi:“MI:0915”(physical association)	0.560
YIPF1	ERGIC3	psi-mi:“MI:0915”(physical association)	0.560
YIPF1	TMPPE	psi-mi:“MI:0915”(physical association)	0.560
YIPF1	TMX2	psi-mi:“MI:0915”(physical association)	0.560
CMTM2	YIPF1	psi-mi:“MI:0915”(physical association)	0.560
ASGR2	YIPF1	psi-mi:“MI:0915”(physical association)	0.560
APCDD1L	YIPF1	psi-mi:“MI:0915”(physical association)	0.560
ZDHHC7	YIPF1	psi-mi:“MI:0915”(physical association)	0.560
RNF5	YIPF1	psi-mi:“MI:0915”(physical association)	0.560
TMX2	YIPF1	psi-mi:“MI:0915”(physical association)	0.560
FFAR3	YIPF1	psi-mi:“MI:0915”(physical association)	0.560
TMEM248	YIPF1	psi-mi:“MI:0915”(physical association)	0.560
TIMMDC1	YIPF1	psi-mi:“MI:0915”(physical association)	0.560
GPR42	YIPF1	psi-mi:“MI:0915”(physical association)	0.560
LEPROT	YIPF1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (63): YIPF6 (Two-hybrid), YIPF1 (Affinity Capture-RNA), YIPF1 (Affinity Capture-RNA), YIPF6 (Affinity Capture-MS), TPM2 (Affinity Capture-MS), YIPF1 (Two-hybrid), YIPF1 (Protein-RNA), YIPF1 (Affinity Capture-RNA), AQP6 (Two-hybrid), SLC7A8 (Two-hybrid), TMEM248 (Two-hybrid), GPRC5D (Two-hybrid), TIMMDC1 (Two-hybrid), ERGIC3 (Two-hybrid), GPR42 (Two-hybrid)

ESM2 similar proteins: A1CJW1, A1D7K7, A1ZA77, A3LU53, A5DGY3, A5JYQ9, A6R3V7, A6ZV87, A7F5K4, A7TSA7, B0XYF0, B2WDD8, B3LIC1, B3M9A8, B3NIN0, B4IAB8, B4PET6, B4QJ33, B4UN04, C6Y4C8, O14225, O14290, O44953, P0CS24, P0CS25, P35180, P35848, P41806, P58684, Q03880, Q0CXF5, Q0UV26, Q1DPX9, Q2HDV5, Q4WX68, Q5B905, Q5RBL0, Q61CQ8, Q6BXM0, Q6CDK3

Diamond homologs: Q54TS4, Q5RBL0, Q5XIT3, Q6P6G5, Q91VU1, Q99LP8, Q9BWQ6, Q9UTD3, Q9Y548

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	47
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1432 predictions. Top by Δscore:

Variant	Effect	Δscore
1:53860054:A:AC	donor_gain	1.0000
1:53860055:C:CT	donor_gain	1.0000
1:53860055:CT:C	donor_gain	1.0000
1:53860055:CTTT:C	donor_gain	1.0000
1:53860149:TATGC:T	acceptor_gain	1.0000
1:53860151:TGCC:T	acceptor_loss	1.0000
1:53860153:CCT:C	acceptor_loss	1.0000
1:53860154:C:CA	acceptor_loss	1.0000
1:53871368:CAA:C	donor_loss	1.0000
1:53871369:AAC:A	donor_loss	1.0000
1:53871370:A:AT	donor_loss	1.0000
1:53871488:CCTG:C	acceptor_loss	1.0000
1:53871489:C:CC	acceptor_gain	1.0000
1:53871490:T:A	acceptor_loss	1.0000
1:53878720:TAA:T	acceptor_gain	1.0000
1:53878728:A:T	acceptor_gain	1.0000
1:53888897:A:C	donor_gain	1.0000
1:53860050:TCTTA:T	donor_loss	0.9900
1:53860051:CTTA:C	donor_loss	0.9900
1:53860052:TTA:T	donor_loss	0.9900
1:53860053:TACT:T	donor_loss	0.9900
1:53860054:AC:A	donor_loss	0.9900
1:53860054:ACTTT:A	donor_gain	0.9900
1:53860055:CTT:C	donor_gain	0.9900
1:53860055:CTTTC:C	donor_gain	0.9900
1:53860058:T:A	donor_gain	0.9900
1:53860067:G:C	donor_gain	0.9900
1:53860151:TGC:T	acceptor_gain	0.9900
1:53860152:GC:G	acceptor_gain	0.9900
1:53860153:CC:C	acceptor_gain	0.9900

AlphaMissense

1997 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:53871480:A:G	W125R	0.997
1:53871480:A:T	W125R	0.997
1:53866879:G:C	P176R	0.996
1:53866879:G:T	P176H	0.996
1:53878391:T:A	R96S	0.996
1:53878391:T:G	R96S	0.996
1:53866789:C:T	G206E	0.995
1:53866797:A:C	C203W	0.995
1:53871476:A:T	I126K	0.995
1:53871488:C:T	G122D	0.995
1:53878320:A:G	L120P	0.995
1:53878392:C:G	R96T	0.995
1:53878660:A:C	F86L	0.995
1:53878660:A:T	F86L	0.995
1:53878662:A:G	F86L	0.995
1:53871442:A:C	S137R	0.994
1:53871442:A:T	S137R	0.994
1:53871444:T:G	S137R	0.994
1:53871476:A:C	I126R	0.994
1:53866799:A:G	C203R	0.993
1:53866889:A:G	W173R	0.993
1:53866889:A:T	W173R	0.993
1:53871379:G:C	F158L	0.993
1:53871379:G:T	F158L	0.993
1:53871381:A:G	F158L	0.993
1:53866790:C:G	G206R	0.992
1:53866790:C:T	G206R	0.992
1:53866912:G:T	A165D	0.992
1:53866913:C:G	A165P	0.992
1:53866798:C:T	C203Y	0.991

dbSNP variants (sampled 300 via entrez): RS1000125411 (1:53862952 C>T), RS1000197616 (1:53864422 T>C), RS1000198653 (1:53879023 A>G), RS1000219304 (1:53883011 T>C), RS1000246903 (1:53863271 A>G), RS1000255851 (1:53869276 C>T), RS1000271583 (1:53882641 T>G), RS1000274752 (1:53859996 T>A,C), RS1000402461 (1:53885584 G>A), RS1000509654 (1:53874130 C>G), RS1000558542 (1:53881586 C>T), RS1000588252 (1:53867607 G>A,C), RS1000654642 (1:53851832 TCTACTGTTCGG>T), RS1000765487 (1:53854242 ACT>A), RS1000820757 (1:53861215 G>T)

Disease associations

OMIM: gene MIM:617521 | 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
GCST001576_1	Nonalcoholic fatty liver disease	5.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol F	affects cotreatment, increases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases expression	1
sodium arsenite	increases expression	1
beta-methylcholine	affects expression	1
Sunitinib	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	affects methylation	1
Benzo(a)pyrene	decreases methylation	1
Dexamethasone	increases expression, affects cotreatment	1
Indomethacin	affects cotreatment, increases expression	1
Ozone	affects expression, increases abundance	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Sodium Selenite	increases expression	1
Antirheumatic Agents	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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