YIF1A

Summary

YIF1A (Yip1 interacting factor homolog A, membrane trafficking protein, HGNC:16688) is a protein-coding gene on chromosome 11q13.2, encoding Protein YIF1A (O95070). Possible role in transport between endoplasmic reticulum and Golgi.

Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport. Located in Golgi apparatus and endoplasmic reticulum-Golgi intermediate compartment.

Source: NCBI Gene 10897 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 72 total
• Druggable target: yes
• MANE Select transcript: NM_020470

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16688
Approved symbol	YIF1A
Name	Yip1 interacting factor homolog A, membrane trafficking protein
Location	11q13.2
Locus type	gene with protein product
Status	Approved
Aliases	YIF1P, 54TM, FinGER7
Ensembl gene	ENSG00000174851
Ensembl biotype	protein_coding
OMIM	611484
Entrez	10897

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 7 protein_coding, 5 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000359461, ENST00000376899, ENST00000376901, ENST00000431556, ENST00000471387, ENST00000474986, ENST00000484814, ENST00000485820, ENST00000494836, ENST00000496746, ENST00000526497, ENST00000528575, ENST00000534374, ENST00000715691

RefSeq mRNA: 2 — MANE Select: NM_020470 NM_001300861, NM_020470

CCDS: CCDS73325, CCDS8132

Canonical transcript exons

ENST00000376901 — 8 exons

Exon	Start	End
ENSE00003508439	66287812	66287916
ENSE00003547691	66288081	66288292
ENSE00003636201	66284873	66284966
ENSE00003679340	66285701	66285758
ENSE00003686935	66285381	66285536
ENSE00003689946	66287598	66287676
ENSE00004027607	66284580	66284783
ENSE00004027608	66288955	66289143

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 98.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 66.3525 / max 286.7559, expressed in 1818 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
120769	39.9199	1813
120768	10.9653	1669
120766	8.0443	1600
120767	6.5161	1602
120765	0.5645	326
120764	0.2079	80
120763	0.1346	47

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	98.00	gold quality
adenohypophysis	UBERON:0002196	97.61	gold quality
right lobe of liver	UBERON:0001114	97.29	gold quality
body of pancreas	UBERON:0001150	96.94	gold quality
mucosa of transverse colon	UBERON:0004991	96.55	gold quality
pituitary gland	UBERON:0000007	96.35	gold quality
left uterine tube	UBERON:0001303	96.29	gold quality
right lobe of thyroid gland	UBERON:0001119	96.21	gold quality
ascending aorta	UBERON:0001496	96.18	gold quality
thoracic aorta	UBERON:0001515	96.14	gold quality
hindlimb stylopod muscle	UBERON:0004252	95.98	gold quality
islet of Langerhans	UBERON:0000006	95.96	gold quality
body of stomach	UBERON:0001161	95.92	gold quality
left lobe of thyroid gland	UBERON:0001120	95.90	gold quality
left coronary artery	UBERON:0001626	95.83	gold quality
right ovary	UBERON:0002118	95.76	gold quality
apex of heart	UBERON:0002098	95.70	gold quality
gastrocnemius	UBERON:0001388	95.54	gold quality
right coronary artery	UBERON:0001625	95.50	gold quality
mucosa of stomach	UBERON:0001199	95.48	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.44	gold quality
lower esophagus	UBERON:0013473	95.42	gold quality
right adrenal gland	UBERON:0001233	95.37	gold quality
tibial nerve	UBERON:0001323	95.37	gold quality
pancreas	UBERON:0001264	95.36	gold quality
body of uterus	UBERON:0009853	95.33	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	95.29	gold quality
transverse colon	UBERON:0001157	95.15	gold quality
left adrenal gland	UBERON:0001234	95.14	gold quality
aorta	UBERON:0000947	95.12	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-HCAD-5	yes	39.44
E-HCAD-13	yes	26.37
E-ANND-3	yes	15.80
E-CURD-112	yes	14.72
E-MTAB-7606	no	371.33
E-MTAB-7052	no	206.20

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• Human Yip1A (YIPF5) interacts with and localizes human Yif1 (YIF1A) to the Golgi apparatus. (PMID:15990086)
• YIF1A is involved in the maintenance of the Golgi structure. (PMID:18718466)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	yif1a	ENSDARG00000019636
mus_musculus	Yif1a	ENSMUSG00000024875
rattus_norvegicus	Yif1a	ENSRNOG00000020201
drosophila_melanogaster	Yif1	FBGN0288631
caenorhabditis_elegans		WBGENE00010178

Paralogs (1): YIF1B (ENSG00000167645)

Protein

Protein identifiers

Protein YIF1A — O95070 (reviewed: O95070)

Alternative names: 54TMp, YIP1-interacting factor homolog A

All UniProt accessions (7): O95070, A6NGW1, C9JST7, E9PIZ0, E9PK42, E9PP02, E9PS11

UniProt curated annotations — full annotation on UniProt →

Function. Possible role in transport between endoplasmic reticulum and Golgi.

Subunit / interactions. Interacts with YIPF5.

Subcellular location. Endoplasmic reticulum membrane. Golgi apparatus membrane. Endoplasmic reticulum-Golgi intermediate compartment membrane.

Similarity. Belongs to the YIF1 family.

RefSeq proteins (2): NP_001287790, NP_065203* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005578	Yif1_fam	Family

Pfam: PF03878

UniProt features (16 total): topological domain 5, transmembrane region 5, modified residue 2, initiator methionine 1, chain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O95070-F1	74.14	0.34

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, 12

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-381038	XBP1(S) activates chaperone genes

MSigDB gene sets: 144 (showing top): REACTOME_UNFOLDED_PROTEIN_RESPONSE_UPR, GOBP_VESICLE_MEDIATED_TRANSPORT, chr11q13, AP1_Q4_01, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOCC_COATED_VESICLE, TGANTCA_AP1_C, NRF2_Q4, RYTTCCTG_ETS2_B, NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON, DANG_BOUND_BY_MYC, NFE2_01, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_ENDOPLASMIC_RETICULUM_GOLGI_INTERMEDIATE_COMPARTMENT_MEMBRANE, GOCC_ENDOPLASMIC_RETICULUM_GOLGI_INTERMEDIATE_COMPARTMENT

GO Biological Process (3): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192)

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

GO Cellular Component (8): Golgi membrane (GO:0000139), endoplasmic reticulum membrane (GO:0005789), endoplasmic reticulum-Golgi intermediate compartment (GO:0005793), Golgi apparatus (GO:0005794), COPII-coated ER to Golgi transport vesicle (GO:0030134), endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
IRE1alpha activates chaperones	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	4
intracellular membrane-bounded organelle	3
transport	2
bounding membrane of organelle	2
endomembrane system	2
intercellular transport	1
intracellular transport	1
Golgi vesicle transport	1
intracellular protein localization	1
establishment of protein localization	1
cellular process	1
binding	1
Golgi apparatus	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
coated vesicle	1
endoplasmic reticulum-Golgi intermediate compartment	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1082 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
YIF1A	YIPF5	Q969M3	986
YIF1A	RAB1A	P11476	719
YIF1A	GOLPH3	Q9H4A6	680
YIF1A	YIPF4	Q9BSR8	675
YIF1A	VTI1B	Q9UEU0	655
YIF1A	YIPF3	Q9GZM5	645
YIF1A	VAPB	O95292	643
YIF1A	YIPF6	Q96EC8	635
YIF1A	SNX1	Q13596	580
YIF1A	YIPF7	Q8N8F6	560
YIF1A	STX5	Q13190	550
YIF1A	PREB	Q9HCU5	549
YIF1A	RABAC1	Q9UI14	548
YIF1A	YIPF2	Q9BWQ6	545
YIF1A	GOLGA2	Q08379	483

IntAct

327 interactions, top by confidence:

A	B	Type	Score
YIF1A	YIPF5	psi-mi:“MI:0915”(physical association)	0.790
YIF1A	TMEM17	psi-mi:“MI:0915”(physical association)	0.660
TMEM9B	DNAJC13	psi-mi:“MI:0914”(association)	0.640
YIF1A	GJA8	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	FAM210B	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	AQP6	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	SCN4B	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	GPR42	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	TMEM248	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	TMX2	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	SCN3B	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	PTGES	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	FFAR2	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	REEP2	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	MSMO1	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	SEC23IP	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	SNX10	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	MYG1	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	NDRG4	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (168): YIF1A (Two-hybrid), YIF1A (Affinity Capture-MS), YIF1A (Affinity Capture-MS), YIF1A (Affinity Capture-MS), YIF1A (Affinity Capture-MS), YIF1A (Affinity Capture-MS), YIF1A (Proximity Label-MS), YIF1A (Proximity Label-MS), YIF1A (Affinity Capture-MS), YIF1A (Affinity Capture-MS), YIF1A (Affinity Capture-MS), YIF1A (Affinity Capture-MS), YIF1A (Affinity Capture-MS), YIF1A (Affinity Capture-MS), YIF1A (Affinity Capture-MS)

ESM2 similar proteins: A2YMP7, A4RE85, B2WCU2, B3M9W1, B3NDM7, B4GRI8, B4HIJ8, B4J043, B4L0H1, B4LIH0, B4MXW6, B4PD01, B4QLP9, O14828, O35609, O95070, P87148, Q0JAI9, Q0UUE1, Q1E5A9, Q29BL9, Q3T196, Q4FZQ0, Q58DR5, Q5APC0, Q5BJH7, Q5RBL0, Q5U3G6, Q60EA5, Q6GN58, Q6P301, Q6P6G5, Q6PC24, Q6Z8F5, Q75IC7, Q7F613, Q7SDN3, Q8H5X5, Q8MRQ4, Q91VU1

Diamond homologs: O95070, P53845, P87148, Q3T196, Q4FZQ0, Q5BJH7, Q5U3G6, Q6GN58, Q6P301, Q6PC24, Q6PEC3, Q91XB7, Q9CX30

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	58
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1544 predictions. Top by Δscore:

Variant	Effect	Δscore
11:66284867:ACTC:A	donor_loss	1.0000
11:66284869:T:TA	donor_loss	1.0000
11:66284871:A:AC	donor_gain	1.0000
11:66284872:C:CC	donor_gain	1.0000
11:66284872:CA:C	donor_gain	1.0000
11:66284872:CAA:C	donor_gain	1.0000
11:66284872:CAAT:C	donor_gain	1.0000
11:66284872:CAATG:C	donor_gain	1.0000
11:66284962:TCATT:T	acceptor_gain	1.0000
11:66284963:CATT:C	acceptor_gain	1.0000
11:66284963:CATTC:C	acceptor_gain	1.0000
11:66284964:ATT:A	acceptor_gain	1.0000
11:66284965:TT:T	acceptor_gain	1.0000
11:66284967:C:CC	acceptor_gain	1.0000
11:66284967:CTGG:C	acceptor_loss	1.0000
11:66284973:G:C	acceptor_gain	1.0000
11:66284973:G:GC	acceptor_gain	1.0000
11:66285375:GCTCA:G	donor_loss	1.0000
11:66285376:CTCA:C	donor_loss	1.0000
11:66285377:TCA:T	donor_loss	1.0000
11:66285378:CACCC:C	donor_loss	1.0000
11:66285379:A:AC	donor_gain	1.0000
11:66285379:AC:A	donor_gain	1.0000
11:66285379:ACC:A	donor_gain	1.0000
11:66285380:C:CA	donor_loss	1.0000
11:66285380:C:CC	donor_gain	1.0000
11:66285380:CC:C	donor_gain	1.0000
11:66285380:CCC:C	donor_gain	1.0000
11:66285380:CCCCA:C	donor_gain	1.0000
11:66285388:A:AC	donor_gain	1.0000

AlphaMissense

1882 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:66285533:G:C	F163L	1.000
11:66285533:G:T	F163L	1.000
11:66285535:A:G	F163L	1.000
11:66285503:G:C	S173R	0.999
11:66285503:G:T	S173R	0.999
11:66285505:T:G	S173R	0.999
11:66285534:A:C	F163C	0.999
11:66285534:A:G	F163S	0.999
11:66285753:C:G	A145P	0.999
11:66287600:G:T	P142H	0.999
11:66287603:A:T	I141N	0.999
11:66287671:C:A	W118C	0.999
11:66287671:C:G	W118C	0.999
11:66288136:G:T	A63D	0.999
11:66284677:G:C	P281R	0.998
11:66284902:A:G	W236R	0.998
11:66284902:A:T	W236R	0.998
11:66285714:C:G	G158R	0.998
11:66285725:C:T	G154E	0.998
11:66285726:C:G	G154R	0.998
11:66285726:C:T	G154R	0.998
11:66285734:A:T	L151H	0.998
11:66287600:G:C	P142R	0.998
11:66287603:A:C	I141S	0.998
11:66287609:A:G	L139P	0.998
11:66287825:G:T	P112H	0.998
11:66287843:A:G	L106P	0.998
11:66287845:C:A	K105N	0.998
11:66287845:C:G	K105N	0.998
11:66287867:T:A	D98V	0.998

dbSNP variants (sampled 300 via entrez): RS1000183080 (11:66286718 C>T), RS1002223555 (11:66288508 A>C), RS1002884122 (11:66288695 C>T), RS1003461071 (11:66285182 C>T), RS1004554132 (11:66285097 A>G), RS1004625574 (11:66286546 G>A), RS1004882011 (11:66290675 T>G), RS1005017782 (11:66291005 C>T), RS1006169265 (11:66286219 G>A), RS1006251445 (11:66287715 G>A,C), RS1006367490 (11:66287123 T>C), RS1007020164 (11:66288392 G>A), RS1007131018 (11:66286055 G>A), RS1007354037 (11:66287052 C>T), RS1007972282 (11:66289226 T>C)

Disease associations

OMIM: gene MIM:611484 | 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
GCST001241_12	Bipolar disorder	2.000000e-07
GCST002726_39	Glucose homeostasis traits	4.000000e-06
GCST008103_21	Bipolar disorder	2.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006831	acute insulin response measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5465281 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.52	Kd	30.01	nM	CHEMBL3752910
7.52	ED50	30.01	nM	CHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 3 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149966: Binding affinity to human YIF1A incubated for 45 mins by Kinobead based pull down assay	kd	0.0300	uM

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, increases methylation	3
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
sodium arsenite	increases abundance, increases expression, affects cotreatment	1
cobaltous chloride	decreases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Atrazine	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Cytarabine	decreases expression	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Fluorouracil	affects response to substance	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Urethane	decreases expression	1
Cyclosporine	decreases expression	1
Thapsigargin	increases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5338433	Binding	Binding affinity to Yif1a (unknown origin) at 200 uM preincubated for 2 hrs followed by pronase addition and measured after 30 mins by coomassie blue staining based SDS-PAGE gel analysis	Structurally Diverse Alkaloids with Anti-Renal-Fibrosis Activity from the Centipede Scolopendra subspinipes mutilans. — J Nat Prod

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3LH	Abcam HEK293T YIF1A KO	Transformed cell line	Female

Clinical trials (associated diseases)

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