ANKRD27 ankyrin repeat domain 27 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ANKRD27provided by HGNC
Official Full Name: ankyrin repeat domain 27provided by HGNC
Primary source: HGNC:HGNC:25310
See related: Ensembl:ENSG00000105186 MIM:618957; AllianceGenome:HGNC:25310
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: VARP; PP12899
Summary: Enables guanyl-nucleotide exchange factor activity and small GTPase binding activity. Involved in endocytic recycling and negative regulation of SNARE complex assembly. Acts upstream of or within early endosome to late endosome transport. Located in endosome; lysosome; and plasma membrane. Implicated in eosinophilic esophagitis. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in testis (RPKM 13.4), thyroid (RPKM 8.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.11

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (32597006..32675180, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (35115771..35193912, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (33087912..33166086, complement)

Chromosome 19 - NC_000019.10 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?

Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29.
Title: Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29.
VARP regulates endosomal trafficking and and retromer-mediated endosome-to-plasma membrane sorting of transmembrane proteins by binding to rab GTP-Binding Proteins and R-SNARE VAMP7 [review].
Title: Multiple Roles of VARP in Endosomal Trafficking: Rabs, Retromer Components and R-SNARE VAMP7 Meet on VARP.
Eosinophilic esophagitis was associate with increased expression of ANKRD27.
Title: GWAS identifies four novel eosinophilic esophagitis loci.
VAMP7-SNARE motif is trapped between Varp and the VAMP7 longin domain, and hence Varp kinetically inhibits the ability of VAMP7 to form SNARE complexes
Title: The binding of Varp to VAMP7 traps VAMP7 in a closed, fusogenically inactive conformation.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
show that TI-VAMP interacts with the Vps9 domain and ankyrin-repeat-containing protein Varp, a guanine nucleotide exchange factor of the small GTPase Rab21, through a specific domain herein called the interacting domain.
Title: Role of Varp, a Rab21 exchange factor and TI-VAMP/VAMP7 partner, in neurite growth.
Varp physically interacts with Rab38, and preferentially binds to the active GTP-bound form of Rab38 both in vitro and in vivo.
Title: Varp interacts with Rab38 and functions as its potential effector.

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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

EBI GWAS Catalog

Description
Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS identifies four novel eosinophilic esophagitis loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

D19S661E (e-PCR)
- UniSTS:150572

D19S607 (e-PCR)
- UniSTS:8140

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase activator activity	IEA Inferred from Electronic Annotation more info
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
enables guanyl-nucleotide exchange factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables guanyl-nucleotide exchange factor activity	IDA Inferred from Direct Assay more info	PubMed
enables guanyl-nucleotide exchange factor activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in early endosome to late endosome transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within early endosome to late endosome transport	IDA Inferred from Direct Assay more info	PubMed
involved_in endocytic recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endosome to melanosome transport	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of SNARE complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in neuron projection morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of dendrite morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of neuron projection development	IEA Inferred from Electronic Annotation more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasmic vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
is_active_in early endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
is_active_in late endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in melanosome	IEA Inferred from Electronic Annotation more info
located_in membrane	HDA more info	PubMed
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in transport vesicle	IBA Inferred from Biological aspect of Ancestor more info
is_active_in tubular endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in tubular endosome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ankyrin repeat domain-containing protein 27

Names: VPS9 domain-containing protein; VPS9-ankyrin-repeat protein; Vps9 domain and ankyrin-repeat-containing protein; ankyrin repeat domain 27 (VPS9 domain)

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_032139.3 → NP_115515.2 ankyrin repeat domain-containing protein 27

See identical proteins and their annotated locations for NP_115515.2

Status: VALIDATED

Source sequence(s)

AA903176, AK054561

Consensus CDS

CCDS32986.1

UniProtKB/Swiss-Prot

Q71MF5, Q86UC3, Q8ND80, Q96NW4, Q9H0I4

Related

ENSP00000304292.3, ENST00000306065.9

Conserved Domains (4) summary

cd00204
Location:738 → 863

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

sd00045
Location:780 → 807

ANK; ANK repeat [structural motif]

pfam02204
Location:264 → 363

VPS9; Vacuolar sorting protein 9 (VPS9) domain

cl26073
Location:567 → 896

Ank_2; Ankyrin repeats (3 copies)