YIPF4

Summary

YIPF4 (Yip1 domain family member 4, HGNC:28145) is a protein-coding gene on chromosome 2p22.3, encoding Protein YIPF4 (Q9BSR8). Involved in the maintenance of the Golgi structure.

Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport and vesicle fusion with Golgi apparatus. Located in Golgi apparatus; endoplasmic reticulum; and plasma membrane.

Source: NCBI Gene 84272 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 35 total
• MANE Select transcript: NM_032312

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28145
Approved symbol	YIPF4
Name	Yip1 domain family member 4
Location	2p22.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC11061, FinGER4, YIPFalpha2
Ensembl gene	ENSG00000119820
Ensembl biotype	protein_coding
OMIM	617534
Entrez	84272

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000238831, ENST00000437765, ENST00000441084, ENST00000495355, ENST00000856768, ENST00000937326, ENST00000951423

RefSeq mRNA: 1 — MANE Select: NM_032312 NM_032312

CCDS: CCDS1781

Canonical transcript exons

ENST00000238831 — 6 exons

Exon	Start	End
ENSE00000809491	32290483	32290636
ENSE00000809492	32292177	32292348
ENSE00000962583	32277904	32278234
ENSE00000962584	32305489	32316594
ENSE00003490808	32301382	32301495
ENSE00003689728	32298234	32298311

Expression profiles

Bgee: expression breadth ubiquitous, 274 present calls, max score 96.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 53.2142 / max 243.9932, expressed in 1824 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
19636	52.2217	1824
19637	0.9206	570
19638	0.0718	29

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	96.92	gold quality
lower esophagus mucosa	UBERON:0035834	94.31	gold quality
adrenal tissue	UBERON:0018303	93.57	gold quality
body of pancreas	UBERON:0001150	92.99	gold quality
ganglionic eminence	UBERON:0004023	92.79	gold quality
stromal cell of endometrium	CL:0002255	92.41	gold quality
cortical plate	UBERON:0005343	92.15	gold quality
ventricular zone	UBERON:0003053	92.05	gold quality
colonic epithelium	UBERON:0000397	90.98	gold quality
pancreas	UBERON:0001264	90.83	gold quality
heart left ventricle	UBERON:0002084	90.65	gold quality
islet of Langerhans	UBERON:0000006	90.31	gold quality
rectum	UBERON:0001052	90.18	gold quality
esophagus mucosa	UBERON:0002469	90.18	gold quality
right lobe of liver	UBERON:0001114	90.07	gold quality
cardiac ventricle	UBERON:0002082	90.07	gold quality
right atrium auricular region	UBERON:0006631	90.02	gold quality
gastrocnemius	UBERON:0001388	89.91	gold quality
muscle of leg	UBERON:0001383	89.58	gold quality
gall bladder	UBERON:0002110	89.49	gold quality
monocyte	CL:0000576	89.20	gold quality
leukocyte	CL:0000738	89.05	gold quality
mucosa of transverse colon	UBERON:0004991	88.93	gold quality
right adrenal gland cortex	UBERON:0035827	88.92	gold quality
mononuclear cell	CL:0000842	88.84	gold quality
endothelial cell	CL:0000115	88.69	silver quality
right adrenal gland	UBERON:0001233	88.64	gold quality
omental fat pad	UBERON:0010414	88.58	gold quality
esophagus	UBERON:0001043	88.57	gold quality
left coronary artery	UBERON:0001626	88.52	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-HCAD-6	no	627.39
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

118 targeting YIPF4, 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-1277-5P	100.00	73.95	5056
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
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-4531	99.99	69.70	3181
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-570-3P	99.96	72.41	4910

Literature-anchored findings (GeneRIF, showing 3)

• YIPF4 was detected as a single mobility form consistent with its predicted molecular weight, three different mobility forms of YIPF3 were detected by western blotting. (PMID:21757827)
• YIPF4 is a binding partner of the papillomavirus E5 proteins. (PMID:26235900)
• The significance of YIPF4 protein for the maintenance of the morphology of the Golgi was tested by RNA interference, revealing a number of specific morphological changes to this organelle on their depletion. (PMID:27999994)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	yipf4	ENSDARG00000030957
mus_musculus	Yipf4	ENSMUSG00000024072
rattus_norvegicus	Yipf4	ENSRNOG00000005610
rattus_norvegicus	Yipf4l1	ENSRNOG00000065148
caenorhabditis_elegans		WBGENE00013365

Paralogs (3): YIPF5 (ENSG00000145817), YIPF7 (ENSG00000177752), YIPF6 (ENSG00000181704)

Protein

Protein identifiers

Protein YIPF4 — Q9BSR8 (reviewed: Q9BSR8)

Alternative names: YIP1 family member 4

All UniProt accessions (3): Q9BSR8, H7C0D5, H7C3X2

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the maintenance of the Golgi structure.

Subunit / interactions. Interacts with YIPF3 and YIPF5. (Microbial infection) Interacts with human papillomavirus (HPV) E5 proteins.

Subcellular location. Golgi apparatus. cis-Golgi network membrane.

Tissue specificity. Expressed in keratinocytes (at protein level).

Similarity. Belongs to the YIP1 family.

RefSeq proteins (1): NP_115688* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006977	Yip1_dom	Domain
IPR045231	Yip1/4-like	Family

Pfam: PF04893

UniProt features (11 total): topological domain 5, transmembrane region 5, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BSR8-F1	70.34	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 161 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, GOBP_VESICLE_ORGANIZATION, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GOBP_MEMBRANE_FUSION, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, GOBP_VESICLE_MEDIATED_TRANSPORT, MARTINEZ_RB1_TARGETS_UP, GOCC_TRANS_GOLGI_NETWORK, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOBP_ORGANELLE_MEMBRANE_FUSION, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, DOUGLAS_BMI1_TARGETS_DN, GFI1_01, GOBP_MEMBRANE_ORGANIZATION, CUI_TCF21_TARGETS_2_DN

GO Biological Process (2): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), vesicle fusion with Golgi apparatus (GO:0048280)

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

GO Cellular Component (6): endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), trans-Golgi network (GO:0005802), plasma membrane (GO:0005886), endomembrane system (GO:0012505), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	3
Golgi vesicle transport	2
endomembrane system	2
intracellular membrane-bounded organelle	2
cellular anatomical structure	2
intercellular transport	1
intracellular transport	1
vesicle fusion	1
Golgi organization	1
binding	1
Golgi apparatus subcompartment	1
membrane	1
cell periphery	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

616 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
YIPF4	YIPF3	Q9GZM5	845
YIPF4	YIPF2	Q9BWQ6	726
YIPF4	YIF1A	O95070	675
YIPF4	YIPF1	Q9Y548	624
YIPF4	ZNF324B	Q6AW86	540
YIPF4	YIF1B	Q5BJH7	461
YIPF4	FRMD5	Q7Z6J6	458
YIPF4	TMPPE	Q6ZT21	451
YIPF4	SLC66A3	Q8N755	422
YIPF4	TMC8	Q8IU68	405
YIPF4	TMEM178B	H3BS89	403
YIPF4	TIRAP	P58753	393
YIPF4	IER3IP1	Q9Y5U9	392
YIPF4	DOLPP1	Q86YN1	385
YIPF4	TMEM41A	Q96HV5	374

IntAct

143 interactions, top by confidence:

A	B	Type	Score
YIPF3	YIPF4	psi-mi:“MI:0915”(physical association)	0.830
YIPF4	YIPF3	psi-mi:“MI:0915”(physical association)	0.830
SLC7A1	YIPF4	psi-mi:“MI:0915”(physical association)	0.740
YIPF4	FATE1	psi-mi:“MI:0915”(physical association)	0.720
FATE1	YIPF4	psi-mi:“MI:0915”(physical association)	0.720
RNF185	YIPF4	psi-mi:“MI:0915”(physical association)	0.560
YIPF4	RNF185	psi-mi:“MI:0915”(physical association)	0.560
YIPF4	IER3IP1	psi-mi:“MI:0915”(physical association)	0.560
SLC35A4	YIPF4	psi-mi:“MI:0915”(physical association)	0.560
TSNARE1	YIPF4	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	YIPF4	psi-mi:“MI:0915”(physical association)	0.560
RNF5	YIPF4	psi-mi:“MI:0915”(physical association)	0.560
ARL6IP1	YIPF4	psi-mi:“MI:0915”(physical association)	0.560
YIPF4	TVP23B	psi-mi:“MI:0915”(physical association)	0.560
YIPF4	NAT8	psi-mi:“MI:0915”(physical association)	0.560
YIPF4	REEP4	psi-mi:“MI:0915”(physical association)	0.560
GPR42	YIPF4	psi-mi:“MI:0915”(physical association)	0.560
	YIPF4	psi-mi:“MI:0915”(physical association)	0.560
SLC10A1	YIPF4	psi-mi:“MI:0915”(physical association)	0.560
SLC7A14	YIPF4	psi-mi:“MI:0915”(physical association)	0.560
YIPF4	ERGIC3	psi-mi:“MI:0915”(physical association)	0.560
SLC30A8	YIPF4	psi-mi:“MI:0915”(physical association)	0.560
SLC18A1	YIPF4	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (95): YIPF4 (Two-hybrid), FATE1 (Two-hybrid), RNF185 (Two-hybrid), YIPF4 (Affinity Capture-MS), YIPF4 (Two-hybrid), YIPF4 (Affinity Capture-RNA), YIPF4 (Affinity Capture-MS), YIPF4 (Affinity Capture-MS), YIPF4 (Affinity Capture-MS), YIPF4 (Affinity Capture-MS), YIPF4 (Affinity Capture-MS), YIPF4 (Affinity Capture-MS), YIPF4 (Affinity Capture-MS), YIPF4 (Affinity Capture-MS), YIPF4 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I3PI99, A0M8U1, A7Y521, B5DEN9, C5HGF3, O88544, O94973, P13666, P17427, P18484, P38024, Q00765, Q0VCK5, Q0X0A5, Q13098, Q1RLU8, Q28635, Q2PG42, Q3KNM2, Q3SZA0, Q3T0N3, Q3T126, Q3T178, Q3ZC24, Q4R5E6, Q5F418, Q5I0H4, Q5M7T4, Q5R648, Q5R9B0, Q5R9M4, Q5RE33, Q5ZJ41, Q5ZJD7, Q6DGW9, Q6GM44, Q6NRT5, Q7TQ48, Q8C407, Q8R1Z9

Diamond homologs: A5D7K7, O94348, P53039, Q4R5M4, Q54QY3, Q5E9E8, Q5R6W5, Q5XID0, Q5ZJD7, Q66KA5, Q6P5I8, Q7SXS2, Q8N8F6, Q969M3, Q9BSR8, Q9EQQ2, Q9JIM5, A6QLC6, O64614, Q28CH8, Q4QQU5, Q54RZ2, Q5M7T4, Q6IQ85, Q6NYF1, Q8BR70, Q8C407, Q93VH1, Q96EC8, Q9P6P8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 82 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
amino acid transport	5	22.3×	1e-03
adenylate cyclase-activating G protein-coupled receptor signaling pathway	6	9.7×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	31
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1009 predictions. Top by Δscore:

Variant	Effect	Δscore
2:32290480:A:AG	acceptor_gain	1.0000
2:32290481:A:AG	acceptor_gain	1.0000
2:32290482:G:GG	acceptor_gain	1.0000
2:32290621:A:G	donor_gain	1.0000
2:32290632:CTCTT:C	donor_gain	1.0000
2:32290635:TT:T	donor_gain	1.0000
2:32290637:G:GG	donor_gain	1.0000
2:32298231:AAGGT:A	acceptor_gain	1.0000
2:32301496:G:GG	donor_gain	1.0000
2:32306831:T:A	acceptor_gain	1.0000
2:32278233:AGGTG:A	donor_loss	0.9900
2:32278234:GGT:G	donor_loss	0.9900
2:32278235:GTGA:G	donor_loss	0.9900
2:32278271:G:GT	donor_gain	0.9900
2:32278305:TGCCG:T	donor_gain	0.9900
2:32278314:G:GA	donor_gain	0.9900
2:32290478:CTAA:C	acceptor_loss	0.9900
2:32290480:AAG:A	acceptor_loss	0.9900
2:32290481:A:AT	acceptor_loss	0.9900
2:32290633:TCTT:T	donor_gain	0.9900
2:32290634:CTT:C	donor_gain	0.9900
2:32290636:TG:T	donor_loss	0.9900
2:32290637:G:T	donor_loss	0.9900
2:32290638:T:TG	donor_loss	0.9900
2:32290641:G:GG	donor_gain	0.9900
2:32298232:A:G	acceptor_gain	0.9900
2:32298309:GAA:G	donor_gain	0.9900
2:32298312:G:GG	donor_gain	0.9900
2:32301492:AAAAG:A	donor_loss	0.9900
2:32301494:AAG:A	donor_loss	0.9900

AlphaMissense

1550 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:32290587:T:A	W62R	1.000
2:32290587:T:C	W62R	1.000
2:32290589:G:C	W62C	1.000
2:32290589:G:T	W62C	1.000
2:32292185:T:C	L81S	1.000
2:32292214:A:G	K91E	1.000
2:32292221:G:C	R93P	1.000
2:32292223:T:C	C94R	1.000
2:32292227:T:A	V95D	1.000
2:32292236:C:A	P98Q	1.000
2:32292283:G:C	D114H	1.000
2:32292284:A:G	D114G	1.000
2:32292284:A:T	D114V	1.000
2:32292289:T:A	W116R	1.000
2:32292289:T:C	W116R	1.000
2:32292292:G:C	G117R	1.000
2:32292292:G:T	G117C	1.000
2:32292293:G:A	G117D	1.000
2:32292296:C:A	P118H	1.000
2:32292296:C:G	P118R	1.000
2:32292299:T:C	L119P	1.000
2:32292305:T:A	V121D	1.000
2:32292308:T:A	V122D	1.000
2:32292311:T:C	L123P	1.000
2:32298258:T:A	W144R	1.000
2:32298258:T:C	W144R	1.000
2:32298267:G:C	G147R	1.000
2:32298268:G:A	G147D	1.000
2:32298282:T:C	F152L	1.000
2:32298284:C:A	F152L	1.000

dbSNP variants (sampled 300 via entrez): RS1000074214 (2:32304612 A>G), RS1000157981 (2:32311414 T>C), RS1000334005 (2:32284088 T>G), RS1000361005 (2:32300033 G>A,C,T), RS1000361167 (2:32299314 A>G), RS1000366918 (2:32294680 G>A,C), RS1000425083 (2:32311729 C>G), RS1000447426 (2:32278573 G>C), RS1000496615 (2:32308727 A>G), RS1000515344 (2:32279556 C>A,T), RS1000515905 (2:32315677 T>A,C), RS1000558093 (2:32277765 G>A,T), RS1000562301 (2:32284940 G>C), RS1000569175 (2:32310112 T>C,G), RS1000636212 (2:32289602 C>T)

Disease associations

OMIM: gene MIM:617534 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST006661_237	Male-pattern baldness	7.000000e-26
GCST006661_313	Male-pattern baldness	2.000000e-20
GCST006661_314	Male-pattern baldness	4.000000e-20
GCST007576_79	Chronotype	4.000000e-09
GCST010002_387	Refractive error	2.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008328	chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases methylation	2
sodium arsenite	decreases expression, increases expression	2
Cyclosporine	increases expression	2
TAK-243	decreases sumoylation	1
dicrotophos	decreases expression	1
11-nor-delta(9)-tetrahydrocannabinol-9-carboxylic acid	affects methylation, increases abundance	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	increases expression	1
abrine	decreases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	increases response to substance, increases expression	1
jinfukang	decreases expression	1
Resveratrol	increases expression, affects cotreatment	1
Sunitinib	increases expression	1
Leflunomide	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Benzo(a)pyrene	affects methylation	1
Cannabinoids	increases abundance, affects methylation	1
Diuron	decreases expression	1
Hydrogen Peroxide	affects cotreatment, decreases expression	1
Ivermectin	decreases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Theophylline	affects cotreatment, decreases expression	1
Valproic Acid	increases expression	1
Aflatoxin M1	decreases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1

Cellosaurus cell lines

4 cell lines: 2 transformed cell line, 1 cancer cell line, 1 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D1J3	HEK293::TMEM192-3xHA YIPF4-/-	Transformed cell line	Female
CVCL_D1J4	HEK293::TMEM192-3xHA YIPF4-/-;YIPF3-/-	Transformed cell line	Female
CVCL_D1J9	HeLa::TMEM192-3xHA YIPF4 KO	Cancer cell line	Female
CVCL_D1KU	H9 AAVS1-TRE3G-NGN2 TMEM192-3xHA YIPF4-/-	Embryonic stem cell	Female

Clinical trials (associated diseases)

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