YIPF5 Yip1 domain family member 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: YIPF5provided by HGNC
Official Full Name: Yip1 domain family member 5provided by HGNC
Primary source: HGNC:HGNC:24877
See related: Ensembl:ENSG00000145817 MIM:611483; AllianceGenome:HGNC:24877
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MEDS2; SB140; SMAP5; YIP1A; SMAP-5; FinGER5; YIPFalpha1A
Summary: Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; regulation of ER to Golgi vesicle-mediated transport; and vesicle fusion with Golgi apparatus. Located in Golgi apparatus; endoplasmic reticulum; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in placenta (RPKM 14.2), thyroid (RPKM 12.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q31.3

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (144158162..144170659, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (144690356..144702848, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (143537726..143550223, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Balanced chromosomal rearrangements implicate YIPF5 and SPATC1L in non-obstructive oligoasthenozoospermia and oligozoospermia and of a derivative chromosome 22 in recurrent miscarriage.
Title: Balanced chromosomal rearrangements implicate YIPF5 and SPATC1L in non-obstructive oligoasthenozoospermia and oligozoospermia and of a derivative chromosome 22 in recurrent miscarriage.
Vitamin D receptor (VDR) mediates the quiescence of activated hepatic stellate cells (aHSCs) by regulating M2 macrophage exosomal smooth muscle cell-associated protein 5 (SMAP-5).
Title: Vitamin D receptor (VDR) mediates the quiescence of activated hepatic stellate cells (aHSCs) by regulating M2 macrophage exosomal smooth muscle cell-associated protein 5 (SMAP-5).
YIPF5 mutations cause neonatal diabetes and microcephaly through endoplasmic reticulum stress.
Title: YIPF5 mutations cause neonatal diabetes and microcephaly through endoplasmic reticulum stress.
YIPF5 positively regulates STING-mediated innate immune responses.
Title: YIPF5 Is Essential for Innate Immunity to DNA Virus and Facilitates COPII-Dependent STING Trafficking.
The significance of YIPF5 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.
Title: Functional characterisation of the YIPF protein family in mammalian cells.
we propose a model for intracellular Brucella replication that exploits the host unfolded protein response and endoplasmic reticulum -derived vacuole formation machineries, both of which depend on Yip1A-mediated IRE1 activation.
Title: Yip1A, a novel host factor for the activation of the IRE1 pathway of the unfolded protein response during Brucella infection.
Findings suggest that the ability of Yip1A to bind its established binding partners may be uncoupled from its ability to control ER whorl formation.
Title: Identification of discrete sites in Yip1A necessary for regulation of endoplasmic reticulum structure.
Results reveal a conserved Yip1A-mediated mechanism for ER membrane organization that may serve to regulate cargo exit from the organelle.
Title: Yip1A structures the mammalian endoplasmic reticulum.
Observational study of gene-disease association. (HuGE Navigator)
Title: Fine mapping of the CELIAC2 locus on chromosome 5q31-q33 in the Finnish and Hungarian populations.
These results suggested that Yip1A has a role in COPI-independent retrograde transport from the Golgi to the ER and regulates the membrane recruitment of Rab6.
Title: Yip1A regulates the COPI-independent retrograde transport from the Golgi complex to the ER.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Microcephaly, epilepsy, and diabetes syndrome 2 MedGen: C5543294 OMIM: 619278 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-AA040621 (e-PCR)
- UniSTS:74792

STS-N40203 (e-PCR)
- UniSTS:71989

L18426 (e-PCR)
- UniSTS:34648

RH45973 (e-PCR)
- UniSTS:80292

STS-N54466 (e-PCR)
- UniSTS:71140

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in insulin processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of ER to Golgi vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of ER to Golgi vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vesicle fusion with Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in COPII-coated ER to Golgi transport vesicle	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info
located_in endoplasmic reticulum exit site	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in trans-Golgi network	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: protein YIPF5

Names: YIP1 family member 5; YPT-interacting protein 1 A; five-pass transmembrane protein localizing in the Golgi apparatus and the endoplasmic reticulum 5; golgi membrane protein SB140; smooth muscle cell associated protein 5

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001024947.4 → NP_001020118.1 protein YIPF5 isoform a

See identical proteins and their annotated locations for NP_001020118.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 encode the same protein (isoform a).

Source sequence(s)

AY640926, AY640928, BP310538

Consensus CDS

CCDS4279.1

UniProtKB/Swiss-Prot

D3DQF5, Q4VSN6, Q53EX4, Q8NHE5, Q969M3, Q9H338, Q9H3U4

UniProtKB/TrEMBL

B3KW34

Related

ENSP00000397704.2, ENST00000448443.6

Conserved Domains (1) summary

cl21557
Location:89 → 257

Yip1; Yip1 domain
NM_001271732.2 → NP_001258661.1 protein YIPF5 isoform b

See identical proteins and their annotated locations for NP_001258661.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate exon in the 5' coding region and uses a downstream start codon, compared to variant 1. It encodes isoform b which has a shorter N-terminus compared to isoform a.

Source sequence(s)

AY640926, AY640929, BP310538

Consensus CDS

CCDS64277.1

UniProtKB/TrEMBL

E5RHH4

Related

ENSP00000425422.1, ENST00000513112.5

Conserved Domains (1) summary

cl21557
Location:35 → 203

Yip1; Yip1 domain
NM_030799.9 → NP_110426.4 protein YIPF5 isoform a

See identical proteins and their annotated locations for NP_110426.4

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein (isoform a).

Source sequence(s)

AY640926, BP310538

Consensus CDS

CCDS4279.1

UniProtKB/Swiss-Prot

D3DQF5, Q4VSN6, Q53EX4, Q8NHE5, Q969M3, Q9H338, Q9H3U4

UniProtKB/TrEMBL

B3KW34

Related

ENSP00000274496.5, ENST00000274496.10

Conserved Domains (1) summary

cl21557
Location:89 → 257

Yip1; Yip1 domain