YIPF6

Summary

YIPF6 (Yip1 domain family member 6, HGNC:28304) is a protein-coding gene on chromosome Xq12-q13.1, encoding Protein YIPF6 (Q96EC8). May be required for stable YIPF1 and YIPF2 protein expression.

Predicted to enable identical protein binding activity. Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport. Predicted to act upstream of or within intestinal epithelial cell development. Located in Golgi apparatus subcompartment and endoplasmic reticulum.

Source: NCBI Gene 286451 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 71 total
• MANE Select transcript: NM_173834

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28304
Approved symbol	YIPF6
Name	Yip1 domain family member 6
Location	Xq12-q13.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC21416, FinGER6, Yip4, YIPFalpha3
Ensembl gene	ENSG00000181704
Ensembl biotype	protein_coding
OMIM	300996
Entrez	286451

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 9 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000374622, ENST00000374643, ENST00000451537, ENST00000462683, ENST00000462972, ENST00000470730, ENST00000496576, ENST00000904195, ENST00000904196, ENST00000904197, ENST00000912111, ENST00000912112, ENST00000912113

RefSeq mRNA: 2 — MANE Select: NM_173834 NM_001195214, NM_173834

CCDS: CCDS14389, CCDS56604

Canonical transcript exons

ENST00000462683 — 7 exons

Exon	Start	End
ENSE00001852921	68531881	68537282
ENSE00001943984	68499051	68499123
ENSE00003495661	68513327	68513405
ENSE00003538912	68518770	68518812
ENSE00003650656	68522760	68522917
ENSE00003657740	68521372	68521497
ENSE00003678043	68511849	68511977

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 99.48.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.8774 / max 115.7985, expressed in 1786 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196590	11.8774	1786

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	99.48	gold quality
medial globus pallidus	UBERON:0002477	97.69	gold quality
oocyte	CL:0000023	97.29	gold quality
parotid gland	UBERON:0001831	97.11	gold quality
globus pallidus	UBERON:0001875	97.06	gold quality
cardia of stomach	UBERON:0001162	97.03	gold quality
tibia	UBERON:0000979	96.92	gold quality
nipple	UBERON:0002030	96.76	gold quality
trabecular bone tissue	UBERON:0002483	96.69	gold quality
bronchial epithelial cell	CL:0002328	96.31	gold quality
type B pancreatic cell	CL:0000169	95.98	gold quality
pylorus	UBERON:0001166	95.68	gold quality
visceral pleura	UBERON:0002401	95.44	gold quality
pericardium	UBERON:0002407	95.34	gold quality
tendon of biceps brachii	UBERON:0008188	95.33	gold quality
epithelium of bronchus	UBERON:0002031	95.30	gold quality
bronchus	UBERON:0002185	95.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	95.21	gold quality
mucosa of paranasal sinus	UBERON:0005030	94.69	gold quality
inferior vagus X ganglion	UBERON:0005363	94.65	gold quality
trigeminal ganglion	UBERON:0001675	94.61	gold quality
biceps brachii	UBERON:0001507	94.59	gold quality
saphenous vein	UBERON:0007318	94.57	gold quality
epithelium of mammary gland	UBERON:0003244	94.56	gold quality
mammary duct	UBERON:0001765	94.39	gold quality
superior vestibular nucleus	UBERON:0007227	94.32	gold quality
lateral globus pallidus	UBERON:0002476	94.26	gold quality
jejunal mucosa	UBERON:0000399	94.25	gold quality
palpebral conjunctiva	UBERON:0001812	94.22	gold quality
renal medulla	UBERON:0000362	94.16	gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-CURD-88	yes	3992.87
E-MTAB-8142	yes	105.43
E-HCAD-9	yes	15.87
E-ANND-3	yes	12.96
E-GEOD-125970	yes	6.80
E-GEOD-134144	no	3486.43
E-CURD-135	no	3145.22
E-GEOD-137537	no	3087.94
E-MTAB-8894	no	2938.18
E-MTAB-6701	no	31.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

224 targeting YIPF6, 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-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-4723-5P	99.97	68.70	2034

Literature-anchored findings (GeneRIF, showing 3)

• YIPF6 overexpression in prostate cancer tumor cell lines resulted in reduced cell proliferation and colony formation. (PMID:28144969)
• 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)
• Levels of YIPF6 protein in human liver correlate with hepatic steatosis and correlate inversely with levels of FGF21 in serum from patients with nonalcoholic fatty liver disease. (PMID:31289229)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	yipf6	ENSDARG00000054433
mus_musculus	Yipf6	ENSMUSG00000047694
rattus_norvegicus	Yipf6	ENSRNOG00000006642
drosophila_melanogaster	CG3652	FBGN0031600
caenorhabditis_elegans	W02D9.2	WBGENE00012208

Paralogs (3): YIPF4 (ENSG00000119820), YIPF5 (ENSG00000145817), YIPF7 (ENSG00000177752)

Protein

Protein identifiers

Protein YIPF6 — Q96EC8 (reviewed: Q96EC8)

Alternative names: YIP1 family member 6

All UniProt accessions (2): B1AV70, Q96EC8

UniProt curated annotations — full annotation on UniProt →

Function. May be required for stable YIPF1 and YIPF2 protein expression.

Subunit / interactions. Predominantly interacts with YIPF1 or YIPF2, but may also form a ternary complex with YIPF1 and YIPF2. This interaction may stabilize YIPF1 and YIPF2.

Subcellular location. Golgi apparatus membrane.

Similarity. Belongs to the YIP1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96EC8-1	1	yes
Q96EC8-2	2

RefSeq proteins (2): NP_001182143, NP_776195* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF04893

UniProt features (18 total): topological domain 6, transmembrane region 5, modified residue 2, initiator methionine 1, chain 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96EC8-F1	74.42	0.28

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 (2): 2, 7

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-432722	Golgi Associated Vesicle Biogenesis

MSigDB gene sets: 181 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, GOBP_EPITHELIAL_CELL_DEVELOPMENT, AREB6_03, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_DIGESTIVE_SYSTEM_DEVELOPMENT, GOCC_TRANS_GOLGI_NETWORK, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, GOBP_INTESTINAL_EPITHELIAL_CELL_DEVELOPMENT, GOCC_COATED_VESICLE, GOBP_INTESTINAL_EPITHELIAL_CELL_DIFFERENTIATION, GOBP_COLUMNAR_CUBOIDAL_EPITHELIAL_CELL_DEVELOPMENT, GOBP_COLUMNAR_CUBOIDAL_EPITHELIAL_CELL_DIFFERENTIATION, BASAKI_YBX1_TARGETS_DN

GO Biological Process (2): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), intestinal epithelial cell development (GO:0060576)

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (10): Golgi trans cisterna (GO:0000138), Golgi membrane (GO:0000139), endoplasmic reticulum (GO:0005783), Golgi medial cisterna (GO:0005797), cis-Golgi network (GO:0005801), trans-Golgi network (GO:0005802), COPII-coated ER to Golgi transport vesicle (GO:0030134), Golgi apparatus (GO:0005794), endomembrane system (GO:0012505), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
trans-Golgi Network Vesicle Budding	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	3
intracellular membrane-bounded organelle	3
Golgi cisterna	2
Golgi apparatus	2
endomembrane system	2
cellular anatomical structure	2
intercellular transport	1
intracellular transport	1
Golgi vesicle transport	1
columnar/cuboidal epithelial cell development	1
intestinal epithelial cell differentiation	1
protein binding	1
binding	1
bounding membrane of organelle	1
Golgi apparatus subcompartment	1
coated vesicle	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

2551 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
YIPF6	STARD8	Q92502	840
YIPF6	ZNF335	Q9H4Z2	772
YIPF6	OPHN1	O60890	705
YIPF6	IER3IP1	Q9Y5U9	695
YIPF6	YIPF3	Q9GZM5	692
YIPF6	YIF1A	O95070	635
YIPF6	YIPF2	Q9BWQ6	618
YIPF6	YIPF5	Q969M3	618
YIPF6	TMEM147	Q9BVK8	593
YIPF6	YIPF7	Q8N8F6	550
YIPF6	YIPF1	Q9Y548	543
YIPF6	EMC7	Q9NPA0	535
YIPF6	ERG28	Q9UKR5	520
YIPF6	FAM98C	Q17RN3	509
YIPF6	NCOA6	Q14686	494
YIPF6	RAB1A	P11476	494

IntAct

316 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
YIPF2	YIPF6	psi-mi:“MI:0915”(physical association)	0.780
YIPF6	YIPF2	psi-mi:“MI:0915”(physical association)	0.780
YIPF6	GJA8	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	CPLX4	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	LYVE1	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	CGRRF1	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	TMX2	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	MTIF3	psi-mi:“MI:0915”(physical association)	0.560
YIPF6		psi-mi:“MI:0915”(physical association)	0.560
YIPF6	TMEM130	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	RAET1L	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	CXorf66	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	TCTA	psi-mi:“MI:0915”(physical association)	0.560
EFNA5	YIPF6	psi-mi:“MI:0915”(physical association)	0.560
TMEM11	YIPF6	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	RNF185	psi-mi:“MI:0915”(physical association)	0.560
CREB3L3	YIPF6	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	SLC38A7	psi-mi:“MI:0915”(physical association)	0.560
RETREG3	YIPF6	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (150): YIPF6 (Two-hybrid), YIPF6 (Two-hybrid), YIPF6 (Two-hybrid), YIPF6 (Affinity Capture-RNA), YIPF6 (Affinity Capture-MS), YIPF6 (Affinity Capture-MS), YIPF6 (Affinity Capture-MS), YIPF6 (Affinity Capture-MS), YIPF6 (Two-hybrid), YIPF6 (Affinity Capture-MS), YIPF6 (Two-hybrid), YIPF6 (Two-hybrid), YIPF6 (Two-hybrid), YIPF6 (Two-hybrid), YIPF6 (Two-hybrid)

ESM2 similar proteins: A0A078H868, A4R0J5, A5D7K7, A6QLC6, B2WDD8, B8JLV7, B9RK42, O64614, O75694, O94348, P37199, Q0IJ20, Q28CH8, Q3B8G4, Q3UDR8, Q4FZQ0, Q4QQU5, Q4R5M4, Q54QY3, Q5BJH7, Q5E9E8, Q5F384, Q5R6W5, Q5U3G6, Q5XID0, Q66KA5, Q6GN58, Q6IQ85, Q6P301, Q6P5I8, Q6PC24, Q6TUD4, Q6ZQE4, Q7SXS2, Q7ZYA0, Q803Z2, Q8BR70, Q8N8F6, Q93VH1, Q93Z32

Diamond homologs: A6QLC6, O64614, Q28CH8, Q4QQU5, Q54RZ2, Q6IQ85, Q6NYF1, Q8BR70, Q93VH1, Q96EC8, Q9P6P8, Q5M7T4, Q5ZJD7, Q8C407, Q9BSR8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	24
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1165 predictions. Top by Δscore:

Variant	Effect	Δscore
X:68511847:A:AG	acceptor_gain	1.0000
X:68511848:G:GG	acceptor_gain	1.0000
X:68511848:GT:G	acceptor_gain	1.0000
X:68511973:CCATC:C	donor_gain	1.0000
X:68511974:CATC:C	donor_gain	1.0000
X:68511974:CATCG:C	donor_loss	1.0000
X:68511975:ATC:A	donor_gain	1.0000
X:68511975:ATCG:A	donor_loss	1.0000
X:68511976:TC:T	donor_gain	1.0000
X:68511976:TCG:T	donor_loss	1.0000
X:68511977:CG:C	donor_loss	1.0000
X:68511978:G:GA	donor_loss	1.0000
X:68511978:G:GG	donor_gain	1.0000
X:68511979:TAAG:T	donor_loss	1.0000
X:68511980:A:AG	donor_loss	1.0000
X:68511982:G:GG	donor_gain	1.0000
X:68513402:GATT:G	donor_gain	1.0000
X:68518808:GCATT:G	donor_gain	1.0000
X:68518809:CATT:C	donor_gain	1.0000
X:68518811:TT:T	donor_gain	1.0000
X:68518813:G:GG	donor_gain	1.0000
X:68521369:CAGA:C	acceptor_loss	1.0000
X:68521370:A:AG	acceptor_gain	1.0000
X:68521370:AGAA:A	acceptor_loss	1.0000
X:68521370:AGAAT:A	acceptor_gain	1.0000
X:68521371:G:GT	acceptor_gain	1.0000
X:68521371:GA:G	acceptor_gain	1.0000
X:68521371:GAA:G	acceptor_gain	1.0000
X:68521371:GAAT:G	acceptor_gain	1.0000
X:68521371:GAATG:G	acceptor_gain	1.0000

AlphaMissense

1542 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:68531967:A:C	S227R	0.998
X:68531969:T:A	S227R	0.998
X:68531969:T:G	S227R	0.998
X:68522773:A:C	S150R	0.997
X:68522775:C:A	S150R	0.997
X:68522775:C:G	S150R	0.997
X:68518778:T:A	W92R	0.996
X:68518778:T:C	W92R	0.996
X:68521445:T:A	W128R	0.996
X:68521445:T:C	W128R	0.996
X:68521452:G:A	G130D	0.996
X:68522796:T:G	C157W	0.996
X:68518781:G:C	G93R	0.995
X:68522779:T:C	C152R	0.995
X:68522780:G:A	C152Y	0.995
X:68531892:T:C	F202L	0.995
X:68531894:C:A	F202L	0.995
X:68531894:C:G	F202L	0.995
X:68513405:T:A	W89R	0.994
X:68513405:T:C	W89R	0.994
X:68518773:A:C	D90A	0.994
X:68518776:T:C	L91S	0.994
X:68521421:T:C	F120L	0.994
X:68521422:T:G	F120C	0.994
X:68521423:T:A	F120L	0.994
X:68521423:T:G	F120L	0.994
X:68522795:G:A	C157Y	0.994
X:68522804:C:G	P160R	0.994
X:68531970:T:A	W228R	0.994
X:68531970:T:C	W228R	0.994

dbSNP variants (sampled 300 via entrez): RS1000421511 (X:68537018 G>A), RS1000490766 (X:68520045 G>T), RS1000529358 (X:68527104 G>C), RS1000604616 (X:68526730 A>C), RS1000672968 (X:68508899 A>T), RS1000824131 (X:68503487 C>G), RS1000882339 (X:68516806 C>T), RS1000895182 (X:68506560 TGTG>T), RS1000931147 (X:68509437 T>G), RS1001180549 (X:68510476 G>C), RS1001184731 (X:68518029 C>T), RS1001240235 (X:68499881 C>T), RS1001243244 (X:68513365 T>C), RS1001253333 (X:68503120 G>A), RS1001289670 (X:68501158 C>G)

Disease associations

OMIM: gene MIM:300996 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST006661_104	Male-pattern baldness	1.000000e-18
GCST006661_233	Male-pattern baldness	5.000000e-61

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
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases methylation	5
sodium arsenite	increases abundance, increases expression, affects cotreatment	2
dicrotophos	decreases expression	1
bisphenol A	affects cotreatment, increases expression	1
beta-lapachone	increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
NSC 689534	increases expression, affects binding	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation	1
Cadmium	increases expression	1
Copper	affects binding, increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Hydrogen Peroxide	affects expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Lead	decreases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Smoke	decreases expression	1
Testosterone	decreases expression	1
Theophylline	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Vanadates	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	increases expression	1
Cadmium Chloride	increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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