Vps13c MGI Mouse Gene Detail - MGI:2444207 - vacuolar protein sorting 13C

Symbol

Vps13c
Name

vacuolar protein sorting 13C
Synonyms

C230055H22Rik

Feature Type

protein coding gene
IDs

MGI:2444207
NCBI Gene: 320528
Alliance

gene page
Transcription Start Sites

8 TSS

Sequence Map

Chr9:67840396-67995638 bp, + strand
From Ensembl annotation of GRCm38

View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 9, 36.77 cM
Mapping Data

2 experiments

SNPs within 2kb

856 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2444207	protein coding gene	Chr9:67840316-67997744 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0034989	protein coding gene	Chr9:67759954-67920826 (+)
A/J	MGP_AJ_G0034969	protein coding gene	Chr9:65428781-65583921 (+)
AKR/J	MGP_AKRJ_G0034899	protein coding gene	Chr9:66974880-67126505 (+)
BALB/cJ	MGP_BALBcJ_G0034962	protein coding gene	Chr9:65166018-65316362 (+)
C3H/HeJ	MGP_C3HHeJ_G0034671	protein coding gene	Chr9:67525149-67674426 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0035481	protein coding gene	Chr9:69609807-69771678 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0032392	protein coding gene	Chr9:65057144-65215121 (+)
CAST/EiJ	MGP_CASTEiJ_G0033993	protein coding gene	Chr9:67750417-67922018 (+)
CBA/J	MGP_CBAJ_G0034643	protein coding gene	Chr9:72001525-72173803 (+)
DBA/2J	MGP_DBA2J_G0034802	protein coding gene	Chr9:65175034-65329516 (+)
FVB/NJ	MGP_FVBNJ_G0034744	protein coding gene	Chr9:64515048-64672203 (+)
LP/J	MGP_LPJ_G0034884	protein coding gene	Chr9:68026945-68184956 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0034786	protein coding gene	Chr9:73174014-73336042 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0035503	protein coding gene	Chr9:67101906-67257168 (+)
PWK/PhJ	MGP_PWKPhJ_G0033697	protein coding gene	Chr9:65415200-65582150 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0033530	protein coding gene	Chr9:67404635-67584989 (+)
WSB/EiJ	MGP_WSBEiJ_G0034105	protein coding gene	Chr9:66996178-67157170 (+)

Human Ortholog

VPS13C, vacuolar protein sorting 13 homolog C

Vertebrate Orthologs

9

Human Ortholog

VPS13C, vacuolar protein sorting 13 homolog C
Orthology source: HomoloGene, HGNC
Synonyms

PARK23
Links

HGNC:23594

NCBI Gene ID: 54832

neXtProt AC: NX_Q709C8

UniProt: Q709C8
Chr Location

15q22.2; chr15:61852389-62060465 (-) GRCh38.p7

HomoloGene

Vertebrate Homology Class 41188
1 human;1 mouse;1 chimpanzee;1 cattle;1 dog;1 chicken;1 zebrafish;1 frog, western clawed;1 macaque, rhesus
HCOP

human homology predictions: VPS13C
Gene Tree

Vps13c

Diseases

1 with human VPS13C associations

				Human Disease	Mouse Models
				Parkinson's disease 23 IDs Parkinson's disease 23 DOID:0060896 ICD10CM:G20 OMIM:616840

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

12 phenotypes from 2 alleles in 2 genetic backgrounds
11 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	immune system	integument	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	neoplasm	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	vision/eye

Click cells to view annotations.

All Mutations and Alleles

15
Chemically induced (other)

1
Gene trapped

10
Targeted

4
Genomic Mutations

1 involving Vps13c
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

112 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

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All GO Annotations

12
GO References

4

External Resources

FuncBase

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell death	cell differentiation	cell population proliferation	cellular component organization	establishment of localization	homeostatic process	immune system process	lipid metabolic process	nucleic acid-templated transcription	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

664
Tissues

19
cDNA Data

10
Literature Summary

5

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase vps13c

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Vps13c interacts with 140 markers (Mir7-1, Mir9-1, Mir9-2, ...) View All

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All Sequences

81
RefSeq

12
UniProt

11
CCDS

CCDS40676.1

Ensembl

ENSMUSG00000035284 (Evidence)
NCBI Gene

320528

			Length	Strain/Species	Flank
genomic	ENSMUSG00000035284	Ensembl Gene Model \| MGI Sequence Detail	155243	C57BL/6J	± kb
transcript	ENSMUST00000077879	Ensembl \| MGI Sequence Detail	11527	Not Applicable
polypeptide	ENSMUSP00000077040	Ensembl \| MGI Sequence Detail	3748	Not Applicable

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UniProt

11 Sequences
Protein Ontology

PR:000017321 vacuolar protein sorting-associated protein 13C

(term hierarchy)
InterPro Domains

IPR015412 Autophagy-related, C-terminal

IPR026847 Vacuolar protein sorting-associated protein 13

IPR031645 Vacuolar protein sorting-associated protein 13, C-terminal

IPR026854 Vacuolar protein sorting-associated protein 13-like, N-terminal domain

IPR031646 Vacuolar protein sorting-associated protein 13, second N-terminal domain

IPR009543 Vacuolar protein sorting-associated protein 13, SHR-binding domain

IPR031642 VPS13, repeated coiled region

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All nucleic 13

Genomic 2

cDNA 10

Primer pair 1

Microarray probesets 4

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MGI:2143091, MGI:2143255, MGI:2143453

Summaries

All 40

Developmental Gene Expression 5

Gene Ontology 4

Phenotypes 11
Earliest

J:80000 The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I & II Team, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002;420:563-573
Latest

J:281311 Nakano Y, et al., Overlapping Activities of Two Neuronal Splicing Factors Switch the GABA Effect from Excitatory to Inhibitory by Regulating REST. Cell Rep. 2019 Apr 16;27(3):860-871.e8

TSS for Vps13c:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr85801	Chr9:67840331-67840358 (+)	-51 bp
Tssr85802	Chr9:67840363-67840372 (+)	-28 bp
Tssr85803	Chr9:67840380-67840383 (+)	-14 bp
Tssr85804	Chr9:67840386-67840429 (+)	12 bp
Tssr85805	Chr9:67840447-67840454 (+)	55 bp
Tssr85808	Chr9:67858827-67858845 (+)	18,440 bp
Tssr85809	Chr9:67858846-67858865 (+)	18,460 bp
Tssr85815	Chr9:67984675-67984678 (+)	144,281 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer & Copyright Notice Send questions and comments to User Support.	last database update 01/12/2021 MGI 6.16