Vps13d MGI Mouse Gene Detail - MGI:2448530 - vacuolar protein sorting 13D

Symbol

Vps13d
Name

vacuolar protein sorting 13D

Feature Type

protein coding gene
IDs

MGI:2448530
NCBI Gene: 230895
Alliance

gene page
Transcription Start Sites

14 TSS

Sequence Map

Chr4:144699192-144921575 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 4, 78.17 cM
Mapping Data

2 experiments

SNPs within 2kb

4209 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2448530	protein coding gene	Chr4:144597619-144921598 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0029101	protein coding gene	Chr4:148339173-148576419 (-)
A/J	MGP_AJ_G0029068	protein coding gene	Chr4:142085211-142310399 (-)
AKR/J	MGP_AKRJ_G0029016	protein coding gene	Chr4:146032015-146258652 (-)
BALB/cJ	MGP_BALBcJ_G0029083	protein coding gene	Chr4:142724854-142949701 (-)
C3H/HeJ	MGP_C3HHeJ_G0028802	protein coding gene	Chr4:146493844-146721517 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0029528	protein coding gene	Chr4:153327642-153557641 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0026780	protein coding gene	Chr4:134809088-135032571 (-)
CAST/EiJ	MGP_CASTEiJ_G0028218	protein coding gene	Chr4:144546969-144784069 (-)
CBA/J	MGP_CBAJ_G0028766	protein coding gene	Chr4:158186294-158421100 (-)
DBA/2J	MGP_DBA2J_G0028914	protein coding gene	Chr4:142238741-142469936 (-)
FVB/NJ	MGP_FVBNJ_G0028876	protein coding gene	Chr4:141377604-141600782 (-)
LP/J	MGP_LPJ_G0029005	protein coding gene	Chr4:148394034-148623980 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0028906	protein coding gene	Chr4:161702040-161934238 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0029565	protein coding gene	Chr4:146527197-146760669 (-)
PWK/PhJ	MGP_PWKPhJ_G0027938	protein coding gene	Chr4:138716868-138945215 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0027772	protein coding gene	Chr4:141762983-141998578 (-)
WSB/EiJ	MGP_WSBEiJ_G0028297	protein coding gene	Chr4:146771533-147011772 (-)

Human Ortholog

VPS13D, vacuolar protein sorting 13 homolog D

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

VPS13D, vacuolar protein sorting 13 homolog D
Synonyms

BLTP5D, SCA24, SCAR4, SCASI
Links

HGNC:23595

NCBI Gene ID: 55187

UniProt: Q5THJ4
Chr Location

1p36.22-p36.21; chr1:12230030-12512047 (+) GRCh38

MGI Vertebrate Homology

Vps13d stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: VPS13D
Gene Tree

Vps13d

Diseases

1 with human VPS13D associations

				Human Disease	Mouse Models
				autosomal recessive spinocerebellar ataxia 4 IDs autosomal recessive spinocerebellar ataxia 4 DOID:0111611 MESH:C537310 OMIM:607317 ORDO:95434 UMLS_CUI:C1846492

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

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Phenotype Summary

2 phenotypes from 1 allele in 1 genetic background
1 phenotype from multigenic genotypes
18 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	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

31
Chemically induced (other)

1
Gene trapped

24
Targeted

5
Transgenic

1
Genomic Mutations

2 involving Vps13d
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

203 strains or lines available

Mice homozygous for a transgenic gene disruption exhibit embryonic lethality at E7.

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All GO Annotations

8
GO References

2

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 differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	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	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	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

728
Tissues

10
cDNA Data

13
Literature Summary

2

Images

Tissue x Stage Matrix

Other Mouse Links

GEO

Expression Atlas
Other Vertebrate Links

Xenbase vps13d

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All Sequences

79
RefSeq

21
UniProt

6
CCDS

CCDS51369.1, CCDS71517.1

Ensembl

ENSMUSG00000020220 (Evidence)
NCBI Gene

230895

			Length	Strain/Species	Flank
genomic	ENSMUSG00000020220	Ensembl Gene Model \| MGI Sequence Detail	222384	C57BL/6J	± kb
transcript	ENSMUST00000036579	Ensembl \| MGI Sequence Detail	15849	Not Applicable
polypeptide	ENSMUSP00000043240	Ensembl \| MGI Sequence Detail	4390	Not Applicable

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UniProt

6 Sequences
InterPro Domains

IPR041969 Intermembrane lipid transfer protein VPS13D, UBA domain

IPR009060 UBA-like superfamily

IPR015940 Ubiquitin-associated domain

IPR026847 Vacuolar protein sorting-associated protein 13

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

IPR009543 Vacuolar protein sorting-associated protein 13, VPS13 adaptor binding domain
GlyGen

B1ART1 9 sites, 8 N-linked glycans (7 sites)

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All nucleic 15

cDNA 14

Primer pair 1

Microarray probesets 7

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MGI:2140701

Summaries

All 42

Developmental Gene Expression 2

Gene Ontology 2

Phenotypes 18
Earliest

J:93290 Araki K, et al., Exchangeable gene trap using the Cre/mutated lox system. Cell Mol Biol (Noisy-Le-Grand). 1999 Jul;45(5):737-50
Latest

J:370619 Miao G, et al., Microglia promote inflammatory cell death upon neuronal mitochondrial impairment during neurodegeneration. Nat Struct Mol Biol. 2025 Jun 25;

TSS for Vps13d:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr44483	Chr4:144921569-144921614 (-)	-17 bp
Tssr44482	Chr4:144921537-144921563 (-)	25 bp
Tssr44481	Chr4:144921523-144921534 (-)	46 bp
Tssr44480	Chr4:144848900-144848904 (-)	72,673 bp
Tssr44479	Chr4:144830340-144830354 (-)	91,228 bp
Tssr44478	Chr4:144823396-144823407 (-)	98,173 bp
Tssr44477	Chr4:144793790-144793799 (-)	127,780 bp
Tssr44476	Chr4:144780817-144780829 (-)	140,752 bp
Tssr44475	Chr4:144751312-144751316 (-)	170,261 bp
Tssr44474	Chr4:144746079-144746086 (-)	175,492 bp
Tssr44473	Chr4:144724897-144724913 (-)	196,670 bp
Tssr44472	Chr4:144710024-144710042 (-)	211,542 bp
Tssr44471	Chr4:144707835-144707849 (-)	213,733 bp
Tssr44470	Chr4:144707362-144707397 (-)	214,195 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, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 03/24/2026 MGI 6.24