YIPF7

Summary

YIPF7 (Yip1 domain family member 7, HGNC:26825) is a protein-coding gene on chromosome 4p12, encoding Protein YIPF7 (Q8N8F6).

Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport and vesicle fusion with Golgi apparatus. Predicted to act upstream of or within Golgi organization. Predicted to be located in cis-Golgi network; endoplasmic reticulum membrane; and endoplasmic reticulum-Golgi intermediate compartment. Predicted to be active in trans-Golgi network.

Source: NCBI Gene 285525 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 52 total
• MANE Select transcript: NM_182592

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26825
Approved symbol	YIPF7
Name	Yip1 domain family member 7
Location	4p12
Locus type	gene with protein product
Status	Approved
Aliases	FLJ39576, FinGER9, Yip1b, YIPFalpha1b
Ensembl gene	ENSG00000177752
Ensembl biotype	protein_coding
OMIM	619754
Entrez	285525

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay

ENST00000332990, ENST00000415895, ENST00000502794, ENST00000508947, ENST00000510035, ENST00000682193, ENST00000682988, ENST00000684034, ENST00000684496, ENST00000684735, ENST00000908026, ENST00000908027, ENST00000953307

RefSeq mRNA: 2 — MANE Select: NM_182592 NM_001387382, NM_182592

CCDS: CCDS54766

Canonical transcript exons

ENST00000415895 — 6 exons

Exon	Start	End
ENSE00001504510	44635922	44636085
ENSE00001646411	44622088	44622576
ENSE00001748160	44629403	44629548
ENSE00001789629	44624601	44624782
ENSE00003704074	44649985	44650101
ENSE00003704556	44651554	44651625

Expression profiles

Bgee: expression breadth ubiquitous, 119 present calls, max score 99.05.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0327 / max 13.1931, expressed in 10 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
51986	0.0327	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
quadriceps femoris	UBERON:0001377	99.05	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.24	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.04	gold quality
skeletal muscle tissue	UBERON:0001134	88.17	gold quality
muscle of leg	UBERON:0001383	86.99	gold quality
gastrocnemius	UBERON:0001388	86.62	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.35	gold quality
cerebellar vermis	UBERON:0004720	77.43	gold quality
muscle tissue	UBERON:0002385	76.94	gold quality
thymus	UBERON:0002370	75.62	silver quality
cerebellar cortex	UBERON:0002129	64.54	gold quality
cerebellum	UBERON:0002037	64.52	gold quality
cerebellar hemisphere	UBERON:0002245	64.51	gold quality
right hemisphere of cerebellum	UBERON:0014890	64.12	gold quality
heart left ventricle	UBERON:0002084	60.93	gold quality
right atrium auricular region	UBERON:0006631	60.78	gold quality
heart	UBERON:0000948	59.11	gold quality
islet of Langerhans	UBERON:0000006	57.45	gold quality
nucleus accumbens	UBERON:0001882	57.22	gold quality
hypothalamus	UBERON:0001898	56.27	gold quality
prefrontal cortex	UBERON:0000451	56.21	gold quality
Brodmann (1909) area 9	UBERON:0013540	55.88	gold quality
brain	UBERON:0000955	55.37	gold quality
calcaneal tendon	UBERON:0003701	55.27	gold quality
frontal cortex	UBERON:0001870	55.17	gold quality
caudate nucleus	UBERON:0001873	55.06	gold quality
anterior cingulate cortex	UBERON:0009835	54.98	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	54.53	gold quality
putamen	UBERON:0001874	54.48	gold quality
cerebral cortex	UBERON:0000956	54.36	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.90

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• GWAS showed intestinal Behcet’s disease-specific associations with an NAALADL2 rs3914501. Down-regulation of NAALADL2 expression was associated with exacerbating intestinal inflammatory responses both in vitro and in vivo. (PMID:28045058)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:123321	ENSDARG00000039726
mus_musculus	Yipf7	ENSMUSG00000029158
rattus_norvegicus	Yipf7	ENSRNOG00000002224
drosophila_melanogaster	Yip1d1	FBGN0032465
caenorhabditis_elegans		WBGENE00009336

Paralogs (3): YIPF4 (ENSG00000119820), YIPF5 (ENSG00000145817), YIPF6 (ENSG00000181704)

Protein

Protein identifiers

Protein YIPF7 — Q8N8F6 (reviewed: Q8N8F6)

Alternative names: Five-pass transmembrane protein localizing in the Golgi apparatus and the endoplasmic reticulum 9, YIP1 family member 7

All UniProt accessions (4): A0A804HK52, A0A804HL09, Q8N8F6, V9GZ30

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Endoplasmic reticulum membrane. Golgi apparatus. cis-Golgi network membrane. trans-Golgi network membrane.

Similarity. Belongs to the YIP1 family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q8N8F6-1	1	yes
Q8N8F6-2	2
Q8N8F6-3	3
Q8N8F6-4	4
Q8N8F6-5	5

RefSeq proteins (1): NP_872398* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF04893

UniProt features (24 total): splice variant 7, topological domain 5, transmembrane region 5, compositionally biased region 2, sequence conflict 2, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N8F6-F1	66.64	0.23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 47 (showing top): GOBP_VESICLE_ORGANIZATION, GOBP_MEMBRANE_FUSION, GOBP_VESICLE_MEDIATED_TRANSPORT, CEBPB_01, chr4p12, GOCC_TRANS_GOLGI_NETWORK, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOBP_ORGANELLE_MEMBRANE_FUSION, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_MEMBRANE_ORGANIZATION, GOBP_ORGANELLE_FUSION, GOBP_GOLGI_ORGANIZATION, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_CIS_GOLGI_NETWORK, GOCC_ENDOPLASMIC_RETICULUM_GOLGI_INTERMEDIATE_COMPARTMENT

GO Biological Process (3): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), vesicle fusion with Golgi apparatus (GO:0048280), Golgi organization (GO:0007030)

GO Molecular Function (0):

GO Cellular Component (9): endoplasmic reticulum membrane (GO:0005789), endoplasmic reticulum-Golgi intermediate compartment (GO:0005793), cis-Golgi network (GO:0005801), trans-Golgi network (GO:0005802), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), endomembrane system (GO:0012505), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	4
intracellular membrane-bounded organelle	4
cellular anatomical structure	3
Golgi vesicle transport	2
endomembrane system	2
intercellular transport	1
intracellular transport	1
vesicle fusion	1
Golgi organization	1
organelle organization	1
endomembrane system organization	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
Golgi apparatus	1
Golgi apparatus subcompartment	1
intracellular anatomical structure	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

566 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
YIPF7	CNBP	P20694	770
YIPF7	DMPK	Q09013	728
YIPF7	YIF1B	Q5BJH7	623
YIPF7	YIPF3	Q9GZM5	606
YIPF7	MBNL1	Q9NR56	593
YIPF7	MBNL2	Q5VZF2	570
YIPF7	YIF1A	O95070	560
YIPF7	YIPF6	Q96EC8	550
YIPF7	MBNL3	Q9NUK0	507
YIPF7	YIPF2	Q9BWQ6	466
YIPF7	NAALADL2	Q58DX5	461
YIPF7	YIPF1	Q9Y548	445
YIPF7	CLCN1	P35523	419
YIPF7	CELF1	Q92879	395
YIPF7	CCDC180	Q9P1Z9	390

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A1CJW1, A1D7K7, A3LU53, A4R0J5, A5DGY3, A6R3V7, A6ZV87, A7F5K4, A7TSA7, A9JTJ0, B2WDD8, B3LIC1, B4UN04, B8JLV7, O64614, P0CS24, P41806, Q08013, Q0CXF5, Q0UV26, Q28CH8, Q28GR4, Q2HDV5, Q3B8G4, Q3SZ87, Q3UDR8, Q42337, Q4V7U1, Q4V8S3, Q5BK13, Q5F384, Q5RAS8, Q5RCD7, Q5SYH2, Q5ZLL0, Q6BXM0, Q6CDK3, Q6CQP9, Q6TUD4, Q75EI3

Diamond homologs: A5D7K7, O94348, P53039, Q4R5M4, Q54QY3, Q5E9E8, Q5R6W5, Q5XID0, Q5ZJD7, Q66KA5, Q6P5I8, Q7SXS2, Q8N8F6, Q969M3, Q9BSR8, Q9EQQ2, Q9JIM5, Q28CH8, Q54RZ2, Q5M7T4, Q8C407

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

52 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

869 predictions. Top by Δscore:

Variant	Effect	Δscore
4:44629387:T:TA	donor_gain	1.0000
4:44635910:T:TA	donor_gain	1.0000
4:44635916:A:C	donor_gain	1.0000
4:44649979:ACTT:A	donor_loss	1.0000
4:44649980:CT:C	donor_loss	1.0000
4:44649981:TTA:T	donor_loss	1.0000
4:44649982:TAC:T	donor_loss	1.0000
4:44649983:A:AC	donor_gain	1.0000
4:44649983:A:T	donor_loss	1.0000
4:44649983:ACTTT:A	donor_gain	1.0000
4:44649984:C:CA	donor_gain	1.0000
4:44649984:C:G	donor_loss	1.0000
4:44649984:CT:C	donor_gain	1.0000
4:44649984:CTT:C	donor_gain	1.0000
4:44649984:CTTT:C	donor_gain	1.0000
4:44649984:CTTTC:C	donor_gain	1.0000
4:44650098:CATC:C	acceptor_gain	1.0000
4:44624599:A:AC	donor_gain	0.9900
4:44624600:C:CC	donor_gain	0.9900
4:44624600:CTG:C	donor_gain	0.9900
4:44629549:C:CC	acceptor_gain	0.9900
4:44635920:A:AC	donor_gain	0.9900
4:44635920:AT:A	donor_gain	0.9900
4:44635920:ATCTT:A	donor_gain	0.9900
4:44636086:C:CC	acceptor_gain	0.9900
4:44649977:GTAC:G	donor_loss	0.9900
4:44649978:TAC:T	donor_loss	0.9900
4:44649980:CTTA:C	donor_gain	0.9900
4:44650099:ATCC:A	acceptor_loss	0.9900
4:44650100:TC:T	acceptor_gain	0.9900

AlphaMissense

1668 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:44622528:A:C	S243R	0.991
4:44622528:A:T	S243R	0.991
4:44622530:T:G	S243R	0.991
4:44624744:A:C	S179R	0.988
4:44624744:A:T	S179R	0.988
4:44624746:T:G	S179R	0.988
4:44622536:A:G	W241R	0.987
4:44622536:A:T	W241R	0.987
4:44624666:G:C	S205R	0.985
4:44624666:G:T	S205R	0.985
4:44624668:T:G	S205R	0.985
4:44622531:A:C	C242W	0.980
4:44622533:A:G	C242R	0.978
4:44624651:G:C	C210W	0.978
4:44624643:G:C	P213R	0.976
4:44622458:A:G	C267R	0.972
4:44622464:A:C	Y265D	0.972
4:44624643:G:T	P213H	0.971
4:44622417:G:C	F280L	0.967
4:44622417:G:T	F280L	0.967
4:44622419:A:G	F280L	0.967
4:44624734:A:G	C183R	0.967
4:44624649:A:G	L211P	0.966
4:44622520:G:T	A246D	0.964
4:44622456:A:C	C267W	0.961
4:44629432:A:G	C157R	0.961
4:44624659:C:G	G208R	0.957
4:44622532:C:T	C242Y	0.955
4:44624653:A:G	C210R	0.955
4:44622521:C:G	A246P	0.954

dbSNP variants (sampled 300 via entrez): RS1000008407 (4:44635519 A>T), RS1000075075 (4:44634091 A>G), RS1000141631 (4:44626807 G>A,C,T), RS1000220018 (4:44658604 T>A,C,G), RS1000226293 (4:44652561 A>C), RS1000277203 (4:44652173 G>A), RS1000280675 (4:44649514 T>A,C), RS1000450128 (4:44636187 T>A,G), RS1000454903 (4:44653361 G>A), RS1000531198 (4:44631522 T>C), RS1000550853 (4:44653995 G>A,C), RS1000729908 (4:44643155 A>G), RS1000809440 (4:44654393 TGTGTTCTACTCATA>T), RS1000893815 (4:44641470 G>T), RS1000959815 (4:44659837 G>C)

Disease associations

OMIM: gene MIM:619754 | 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
GCST002783_2	Body mass index	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects cotreatment	1
CGP 52608	affects binding, increases reaction	1
bisphenol S	affects cotreatment, decreases methylation	1
incobotulinumtoxinA	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Cadmium	decreases expression, increases abundance	1
Lipopolysaccharides	affects cotreatment, increases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression, increases abundance	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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