YIPF2

Summary

YIPF2 (Yip1 domain family member 2, HGNC:28476) is a protein-coding gene on chromosome 19p13.2, encoding Protein YIPF2 (Q9BWQ6).

Predicted to enable small GTPase binding activity. Predicted to be involved in vesicle-mediated transport. Located in Golgi apparatus subcompartment and transport vesicle.

Source: NCBI Gene 78992 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 85 total
• MANE Select transcript: NM_001321439

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28476
Approved symbol	YIPF2
Name	Yip1 domain family member 2
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC3262, FinGER2, Yip5C, YIPFbeta3B
Ensembl gene	ENSG00000130733
Ensembl biotype	protein_coding
OMIM	617522
Entrez	78992

Gene structure

Transcript identifiers

Ensembl transcripts: 40 — 38 protein_coding, 2 retained_intron

ENST00000253031, ENST00000585858, ENST00000586575, ENST00000586748, ENST00000587943, ENST00000588347, ENST00000588962, ENST00000589971, ENST00000590329, ENST00000591872, ENST00000592505, ENST00000592646, ENST00000874113, ENST00000874114, ENST00000874115, ENST00000874116, ENST00000874117, ENST00000874118, ENST00000874119, ENST00000874120, ENST00000874121, ENST00000874122, ENST00000874123, ENST00000874124, ENST00000874125, ENST00000874127, ENST00000874128, ENST00000874130, ENST00000874131, ENST00000922038, ENST00000922039, ENST00000922040, ENST00000922041, ENST00000922042, ENST00000971374, ENST00000971375, ENST00000971376, ENST00000971377, ENST00000971378, ENST00000971379

RefSeq mRNA: 3 — MANE Select: NM_001321439 NM_001321439, NM_001321440, NM_024029

CCDS: CCDS12251, CCDS82293

Canonical transcript exons

ENST00000586748 — 10 exons

Exon	Start	End
ENSE00001061137	10922193	10923174
ENSE00002896830	10928511	10928639
ENSE00003472721	10927630	10927716
ENSE00003522764	10928380	10928440
ENSE00003523968	10927799	10927959
ENSE00003534724	10924076	10924192
ENSE00003556653	10925686	10925773
ENSE00003575312	10923272	10923407
ENSE00003594786	10923495	10923677
ENSE00003786249	10923833	10923999

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 97.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.6976 / max 248.9993, expressed in 1816 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179182	26.4820	1816
179181	1.4333	432
179183	0.5411	309
179180	0.2411	147

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
type B pancreatic cell	CL:0000169	97.50	gold quality
adenohypophysis	UBERON:0002196	97.03	gold quality
pituitary gland	UBERON:0000007	96.64	gold quality
left testis	UBERON:0004533	96.11	gold quality
body of pancreas	UBERON:0001150	95.89	gold quality
right testis	UBERON:0004534	95.78	gold quality
stromal cell of endometrium	CL:0002255	95.37	gold quality
testis	UBERON:0000473	94.35	gold quality
lower esophagus mucosa	UBERON:0035834	94.34	gold quality
minor salivary gland	UBERON:0001830	94.13	gold quality
right uterine tube	UBERON:0001302	93.94	gold quality
saliva-secreting gland	UBERON:0001044	93.82	gold quality
endometrium epithelium	UBERON:0004811	93.81	gold quality
right lobe of thyroid gland	UBERON:0001119	93.79	gold quality
left lobe of thyroid gland	UBERON:0001120	93.44	gold quality
mucosa of transverse colon	UBERON:0004991	93.39	gold quality
mouth mucosa	UBERON:0003729	93.14	gold quality
thyroid gland	UBERON:0002046	92.94	gold quality
endocervix	UBERON:0000458	92.88	gold quality
ascending aorta	UBERON:0001496	92.72	gold quality
gall bladder	UBERON:0002110	92.68	gold quality
thoracic aorta	UBERON:0001515	92.65	gold quality
left adrenal gland	UBERON:0001234	92.60	gold quality
right adrenal gland	UBERON:0001233	92.54	gold quality
left adrenal gland cortex	UBERON:0035825	92.42	gold quality
pancreas	UBERON:0001264	92.41	gold quality
ectocervix	UBERON:0012249	92.37	gold quality
metanephros cortex	UBERON:0010533	92.31	gold quality
esophagus mucosa	UBERON:0002469	92.18	gold quality
right adrenal gland cortex	UBERON:0035827	92.09	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.09

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting YIPF2, 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-4692	100.00	67.32	2066
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-1251-3P	99.64	67.21	1408
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-4761-5P	99.51	66.69	804
HSA-MIR-153-3P	98.96	72.51	1644
HSA-MIR-6887-5P	98.56	68.49	1295
HSA-MIR-6795-5P	98.52	68.51	1277
HSA-MIR-6827-5P	98.46	64.88	1256
HSA-MIR-3121-5P	97.30	66.62	1146
HSA-MIR-4707-3P	86.55	62.02	99

Literature-anchored findings (GeneRIF, showing 2)

• YIPF2 is a new trafficking determinant essential for CD147 glycosylation and transport. YIPF2-controlled ER-Golgi trafficking signature promotes CD147-medated malignant phenotypes in hepatocellular carcinoma. (PMID:31189879)
• YIPF2 promotes chemotherapeutic agent-mediated apoptosis via enhancing TNFRSF10B recycling to plasma membrane in non-small cell lung cancer cells. (PMID:32303681)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	yipf2	ENSDARG00000021399
mus_musculus	Yipf2	ENSMUSG00000032182
rattus_norvegicus	Yipf2	ENSRNOG00000022043
drosophila_melanogaster	CG4645	FBGN0030435
caenorhabditis_elegans		WBGENE00021294

Paralogs (1): YIPF1 (ENSG00000058799)

Protein

Protein identifiers

Protein YIPF2 — Q9BWQ6 (reviewed: Q9BWQ6)

Alternative names: YIP1 family member 2

All UniProt accessions (9): Q9BWQ6, K7EIP7, K7EJN9, K7EL70, K7EM92, K7ENM8, K7ENZ5, K7EQH3, K7ERW0

UniProt curated annotations — full annotation on UniProt →

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

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

Similarity. Belongs to the YIP1 family.

RefSeq proteins (3): NP_001308368, NP_001308369, NP_076934 (=MANE)

Domains & families (InterPro)

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

Pfam: PF04893

UniProt features (16 total): topological domain 6, transmembrane region 5, initiator methionine 1, chain 1, region of interest 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BWQ6-F1	75.81	0.41

Functional residue map

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

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 105 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, GOBP_VESICLE_MEDIATED_TRANSPORT, GOMF_GTPASE_BINDING, CTATGCA_MIR153, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5, GOCC_TRANS_GOLGI_NETWORK, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP, GOCC_LATE_ENDOSOME_MEMBRANE, GOCC_GOLGI_STACK, GOCC_GOLGI_CISTERNA, chr19p13, GOCC_ORGANELLE_SUBCOMPARTMENT

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 (10): Golgi trans cisterna (GO:0000138), Golgi apparatus (GO:0005794), Golgi medial cisterna (GO:0005797), trans-Golgi network (GO:0005802), transport vesicle (GO:0030133), late endosome membrane (GO:0031902), Golgi membrane (GO:0000139), endosome (GO:0005768), endomembrane system (GO:0012505), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

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

Protein interactions and networks

STRING

430 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
YIPF2	YIPF3	Q9GZM5	810
YIPF2	MRPL58	Q14197	761
YIPF2	YIPF4	Q9BSR8	726
YIPF2	MORC2	Q9Y6X9	694
YIPF2	YIPF1	Q9Y548	618
YIPF2	YIPF6	Q96EC8	618
YIPF2	ZNF274	Q96GC6	593
YIPF2	GDF5	P43026	552
YIPF2	YIF1A	O95070	545
YIPF2	MLXIPL	Q9NP71	513
YIPF2	YIPF5	Q969M3	501
YIPF2	NOG	Q13253	489
YIPF2	ARID5B	Q14865	486
YIPF2	MORC1	Q86VD1	479
YIPF2	YIPF7	Q8N8F6	466
YIPF2	TTN	Q8WZ42	466

IntAct

86 interactions, top by confidence:

A	B	Type	Score
YIPF2	YIPF6	psi-mi:“MI:0915”(physical association)	0.780
YIPF6	YIPF2	psi-mi:“MI:0915”(physical association)	0.780
RNF185	YIPF2	psi-mi:“MI:0915”(physical association)	0.720
RNF5	YIPF2	psi-mi:“MI:0915”(physical association)	0.720
YIPF2	RNF185	psi-mi:“MI:0915”(physical association)	0.720
YIPF2	RNF5	psi-mi:“MI:0915”(physical association)	0.720
YIPF2	ACTA2	psi-mi:“MI:0915”(physical association)	0.590
YIPF2	LEPROTL1	psi-mi:“MI:0915”(physical association)	0.560
YIPF2	TMX2	psi-mi:“MI:0915”(physical association)	0.560
YIPF2	TMEM143	psi-mi:“MI:0915”(physical association)	0.560
YIPF2	STING1	psi-mi:“MI:0915”(physical association)	0.560
YIPF2	GPR42	psi-mi:“MI:0915”(physical association)	0.560
SLC30A2	YIPF2	psi-mi:“MI:0915”(physical association)	0.560
	YIPF2	psi-mi:“MI:0915”(physical association)	0.560
YIPF2	ERGIC3	psi-mi:“MI:0915”(physical association)	0.560
MFSD14B	YIPF2	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (52): YIPF2 (Two-hybrid), RNF185 (Two-hybrid), YIPF6 (Two-hybrid), ACTA2 (Affinity Capture-MS), APOB (Affinity Capture-MS), YIPF6 (Two-hybrid), YIPF2 (Two-hybrid), FATE1 (Two-hybrid), ACTA2 (Affinity Capture-MS), YIPF2 (Two-hybrid), YIPF2 (Two-hybrid), YIPF2 (Two-hybrid), YIPF2 (Two-hybrid), YIPF2 (Two-hybrid), YIPF2 (Two-hybrid)

ESM2 similar proteins: A0A2K3D1C8, A0A2K3DU55, A0JMH2, A2YQ58, A8ID74, A8IF44, A8ITV9, A8J1V4, A8JAF2, D0N4E2, E6ZZ11, F5A894, O80952, P22185, Q05B87, Q0C8L9, Q0D3F2, Q0VCH8, Q2QPW2, Q39586, Q3S2U3, Q4VKB4, Q53JI9, Q5GA22, Q5N9A1, Q5U2V5, Q6EU10, Q6PI78, Q6R2V6, Q6Z4A7, Q75BG6, Q75CX4, Q7SEE1, Q80ZM8, Q84V18, Q8GTZ9, Q8GVC7, Q8H8U0, Q8MZC4, Q8RVC7

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

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 26 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.

Reactome pathways:

Pathway	Partners	Fold	FDR
Transport of small molecules	5	9.7×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	66
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2553 predictions. Top by Δscore:

Variant	Effect	Δscore
19:10919239:AT:A	acceptor_gain	1.0000
19:10919582:T:TA	acceptor_gain	1.0000
19:10919590:CCCAG:C	acceptor_loss	1.0000
19:10919591:CCAG:C	acceptor_loss	1.0000
19:10919593:A:AG	acceptor_gain	1.0000
19:10919593:AG:A	acceptor_gain	1.0000
19:10919594:G:GG	acceptor_gain	1.0000
19:10919594:GG:G	acceptor_gain	1.0000
19:10919594:GGAC:G	acceptor_gain	1.0000
19:10919594:GGACA:G	acceptor_gain	1.0000
19:10919676:CACAG:C	donor_loss	1.0000
19:10919681:GTACT:G	donor_loss	1.0000
19:10920547:G:T	donor_gain	1.0000
19:10920572:AGGT:A	donor_loss	1.0000
19:10920573:GGTG:G	donor_loss	1.0000
19:10920574:GTGCG:G	donor_loss	1.0000
19:10920575:T:G	donor_loss	1.0000
19:10920650:T:TA	acceptor_gain	1.0000
19:10920653:CCGCA:C	acceptor_loss	1.0000
19:10920654:CGCAG:C	acceptor_loss	1.0000
19:10920655:GCAG:G	acceptor_loss	1.0000
19:10920656:CAG:C	acceptor_loss	1.0000
19:10920657:A:AG	acceptor_gain	1.0000
19:10920657:AGAC:A	acceptor_loss	1.0000
19:10920658:G:GT	acceptor_gain	1.0000
19:10920658:GAC:G	acceptor_gain	1.0000
19:10920658:GACA:G	acceptor_gain	1.0000
19:10920715:G:GG	donor_gain	1.0000
19:10920746:TAGGT:T	donor_loss	1.0000
19:10920747:AGGT:A	donor_loss	1.0000

AlphaMissense

2013 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:10927648:A:C	F87L	0.989
19:10927648:A:T	F87L	0.989
19:10927650:A:G	F87L	0.989
19:10923954:G:T	P177H	0.985
19:10924083:G:C	F159L	0.985
19:10924083:G:T	F159L	0.985
19:10924085:A:G	F159L	0.985
19:10924184:A:G	W126R	0.985
19:10924184:A:T	W126R	0.985
19:10925763:C:G	R97P	0.985
19:10924171:G:T	T130K	0.983
19:10923954:G:C	P177R	0.982
19:10924192:C:T	G123D	0.979
19:10927650:A:T	F87I	0.979
19:10923864:C:T	G207D	0.978
19:10924171:G:C	T130R	0.977
19:10924084:A:C	F159C	0.975
19:10927649:A:C	F87C	0.973
19:10927662:A:C	Y83D	0.972
19:10923865:C:G	G207R	0.969
19:10923964:A:G	W174R	0.969
19:10923964:A:T	W174R	0.969
19:10924178:A:G	C128R	0.969
19:10927649:A:G	F87S	0.969
19:10923872:G:C	C204W	0.968
19:10923973:A:G	C171R	0.967
19:10924140:G:C	N140K	0.967
19:10924140:G:T	N140K	0.967
19:10924084:A:G	F159S	0.966
19:10925689:A:C	Y122D	0.966

dbSNP variants (sampled 300 via entrez): RS1000128864 (19:10926584 T>G), RS1000202760 (19:10925652 T>C), RS1000292949 (19:10922976 T>C), RS1000293261 (19:10930246 T>C,G), RS1000310241 (19:10924622 T>A), RS1000499554 (19:10922280 C>T), RS1000622819 (19:10928856 C>G,T), RS1000717211 (19:10928703 CT>C), RS1000793182 (19:10927346 A>G,T), RS1000855799 (19:10928782 G>A,C), RS1000980474 (19:10922479 A>C), RS1001512991 (19:10929892 G>A), RS1001773810 (19:10930025 C>G), RS1001949803 (19:10928469 TC>T,TCC), RS1002254766 (19:10928633 C>G)

Disease associations

OMIM: gene MIM:617522 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

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
aristolochic acid I	decreases expression	1
sodium arsenite	increases expression	1
benzo(e)pyrene	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
(+)-JQ1 compound	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Caffeine	increases phosphorylation	1
Doxorubicin	decreases expression	1
Methapyrilene	increases methylation	1
Smoke	decreases expression	1
Dronabinol	decreases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	increases expression	1
Valproic Acid	increases methylation	1
Cadmium Chloride	decreases expression	1
tert-Butylhydroperoxide	decreases expression	1

Clinical trials (associated diseases)

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