Cln5 MGI Mouse Gene Detail - MGI:2442253 - ceroid-lipofuscinosis, neuronal 5

Symbol

Cln5
Name

ceroid-lipofuscinosis, neuronal 5
Synonyms

A730075N08Rik

Feature Type

protein coding gene
IDs

MGI:2442253
NCBI Gene: 211286
Alliance

gene page
Transcription Start Sites

8 TSS

Sequence Map

Chr14:103307679-103315064 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 14, 51.71 cM
Mapping Data

3 experiments

SNPs within 2kb

309 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2442253	protein coding gene	Chr14:103307652-103315064 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0021628	protein coding gene	Chr14:99559747-99567115 (+)
A/J	MGP_AJ_G0021586	protein coding gene	Chr14:96267342-96274705 (+)
AKR/J	MGP_AKRJ_G0021562	protein coding gene	Chr14:99147014-99154377 (+)
BALB/cJ	MGP_BALBcJ_G0021592	protein coding gene	Chr14:96618256-96625619 (+)
C3H/HeJ	MGP_C3HHeJ_G0021370	protein coding gene	Chr14:99048072-99055435 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0022032	protein coding gene	Chr14:103572248-103584893 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0019572	protein coding gene	Chr14:93141068-93148481 (+)
CAST/EiJ	MGP_CASTEiJ_G0020887	protein coding gene	Chr14:96388686-96396064 (+)
CBA/J	MGP_CBAJ_G0021338	protein coding gene	Chr14:107290709-107298072 (+)
DBA/2J	MGP_DBA2J_G0021462	protein coding gene	Chr14:95763924-95771287 (+)
FVB/NJ	MGP_FVBNJ_G0021439	protein coding gene	Chr14:94742221-94749597 (+)
LP/J	MGP_LPJ_G0021530	protein coding gene	Chr14:100376434-100385974 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0021466	protein coding gene	Chr14:110143824-110151187 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0022055	protein coding gene	Chr14:98668282-98675637 (+)
PWK/PhJ	MGP_PWKPhJ_G0020630	protein coding gene	Chr14:92758855-92766226 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0020468	protein coding gene	Chr14:94716142-94723518 (+)
WSB/EiJ	MGP_WSBEiJ_G0020940	protein coding gene	Chr14:99327618-99335704 (+)

Human Ortholog

CLN5, CLN5 intracellular trafficking protein

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CLN5, CLN5 intracellular trafficking protein
Links

HGNC:2076

NCBI Gene ID: 1203

neXtProt AC: NX_O75503

UniProt: O75503
Chr Location

13q22.3; chr13:76990660-77019143 (+) GRCh38

MGI Vertebrate Homology

Cln5 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: CLN5
Gene Tree

Cln5

Diseases

1 with Cln5 mouse models; 1 with human CLN5 associations

Human Disease

Mouse Models

neuronal ceroid lipofuscinosis 5

IDs

View 1 model

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

Mutations/Alleles

1 with disease annotations

References

1 with disease annotations

less

Phenotype Summary

3 phenotypes from 1 allele in 1 genetic background
19 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

7
Chemically induced (other)

1
Endonuclease-mediated

2
Targeted

4
Genomic Mutations

1 involving Cln5
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

15 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous mutants showed loss of vision and accumulation of autofluorescent storage material in the central nervous system. Loss of a subset of GABAergic interneurons was seen in several brain areas.

less

All GO Annotations

47
GO References

10

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.

less

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

828
Tissues

69
cDNA Data

15
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 cln5

ZFIN cln5

less

All Sequences

67
RefSeq

3
UniProt

3
CCDS

CCDS27314.1

Ensembl

ENSMUSG00000022125 (Evidence)
NCBI Gene

211286

			Length	Strain/Species	Flank
genomic	211286	NCBI Gene Model \| MGI Sequence Detail	7386	C57BL/6J	± kb
transcript	NM_001033242	RefSeq \| MGI Sequence Detail	2418	C57BL/6
polypeptide	Q3UMW8	UniProt \| EBI \| MGI Sequence Detail	341	Not Applicable

less

UniProt

3 Sequences
Protein Ontology

PR:000005592 ceroid-lipofuscinosis neuronal protein 5

(term hierarchy)
EC

2.3.1.-, 3.1.2.22
InterPro Domains

IPR026138 Ceroid-lipofuscinosis neuronal protein 5
GlyGen

Q3UMW8 7 sites, 4 N-linked glycans (3 sites)

less

All nucleic 18

cDNA 15

Primer pair 2

Other 1

Microarray probesets 3

Summaries

All 50

Developmental Gene Expression 5

Diseases 1

Gene Ontology 10

Phenotypes 19
Earliest

J:78120 Peterson KA, et al., Functional and comparative genomic analysis of the piebald deletion region of mouse chromosome 14. Genomics. 2002 Aug;80(2):172-84
Latest

J:343112 Luebben AV, et al., Cln5 represents a new type of cysteine-based S-depalmitoylase linked to neurodegeneration. Sci Adv. 2022 Apr 15;8(15):eabj8633

TSS for Cln5:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr127053	Chr14:103307658-103307669 (+)	-15 bp
Tssr127054	Chr14:103307671-103307692 (+)	3 bp
Tssr127055	Chr14:103307695-103307784 (+)	61 bp
Tssr127056	Chr14:103310702-103310732 (+)	3,038 bp
Tssr127057	Chr14:103310781-103310795 (+)	3,109 bp
Tssr127058	Chr14:103311753-103311766 (+)	4,081 bp
Tssr127059	Chr14:103311829-103311844 (+)	4,158 bp
Tssr127060	Chr14:103313352-103313385 (+)	5,690 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 11/12/2024 MGI 6.24