Ccdc40 MGI Mouse Gene Detail - MGI:2443893 - coiled-coil domain containing 40

Symbol

Ccdc40
Name

coiled-coil domain containing 40
Synonyms

B930008I02Rik

Feature Type

protein coding gene
IDs

MGI:2443893
NCBI Gene: 207607
Alliance

genome feature page
Transcription Start Sites

2 TSS

Sequence Map

Chr11:119119398-119156064 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 11, 83.35 cM
Mapping Data

1 experiment

SNPs within 2kb

1120 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2443893	protein coding gene	Chr11:119119328-119156074 (+)
129S1/SvImJ	ENSMUSG00200049902	protein coding gene	Chr11:116487181-116523937 (+)
A/J	ENSMUSG00195029341	protein coding gene	Chr11:116162140-116198890 (+)
AKR/J	ENSMUSG00220024194	protein coding gene	Chr11:116312533-116349284 (+)
BALB/cJ	ENSMUSG00180049426	protein coding gene	Chr11:116455980-116492640 (+)
C3H/HeJ	ENSMUSG00175032756	protein coding gene	Chr11:116413514-116450147 (+)
C57BL/6NJ	ENSMUSG00215045933	protein coding gene	Chr11:115982725-116019482 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017493	protein coding gene	Chr11:115123862-115161380 (+)
CAST/EiJ	ENSTCUG00005033245	protein coding gene	Chr11:115839175-115876064 (+)
CBA/J	ENSMUSG00210047954	protein coding gene	Chr11:116127608-116164236 (+)
DBA/2J	ENSMUSG00185022022	protein coding gene	Chr11:116440708-116477345 (+)
FVB/NJ	ENSMUSG00205023879	protein coding gene	Chr11:116288967-116325755 (+)
JF1/MsJ	ENSUMUG00000044033	protein coding gene	Chr11:116732597-116770596 (+)
LP/J	ENSMUSG00230050274	protein coding gene	Chr11:117506578-117543207 (+)
NOD/ShiLtJ	ENSMUSG00190031711	protein coding gene	Chr11:116511149-116547912 (+)
NZO/HlLtJ	ENSMUSG00225053224	protein coding gene	Chr11:119654806-119691565 (+)
PWK/PhJ	ENSLUMG00010019869	protein coding gene	Chr11:116244299-116282252 (+)
SPRET/EiJ	ENSMSPG00010037646	protein coding gene	Chr11:116820462-116863941 (+)
WSB/EiJ	ENSIUOG00005042832	protein coding gene	Chr11:116247547-116284313 (+)

Human Ortholog

CCDC40, coiled-coil domain 40 molecular ruler complex subunit

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CCDC40, coiled-coil domain 40 molecular ruler complex subunit
Synonyms

CFAP172, CILD15, FAP172
Links

HGNC:26090

NCBI Gene ID: 55036

UniProt: Q4G0X9
Chr Location

17q25.3; chr17:80036632-80100613 (+) GRCh38

MGI Vertebrate Homology

Ccdc40 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: CCDC40
Gene Tree

Ccdc40

Diseases

1 with human CCDC40 associations

				Human Disease	Mouse Models
				primary ciliary dyskinesia 15 IDs primary ciliary dyskinesia 15 DOID:0110623 ICD10CM:Q34.8 OMIM:613808

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

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Phenotype Summary

11 phenotypes from 2 alleles in 2 genetic backgrounds
1 phenotype from multigenic genotypes
12 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 (ENU)

1
Endonuclease-mediated

3
Targeted

3
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

50 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for an ENU-induced allele exhibit heterotaxia, hydrocephalus, short embryonic cilia, and postnatal lethality.

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All GO Annotations

36
GO References

10

Molecular Function

No experimental evidence to support Molecular Function annotation, following literature review. See J:73796.

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

668
Tissues

11
cDNA Data

23
Literature Summary

3

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase ccdc42.2

ZFIN ccdc40

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All Sequences

58
RefSeq

15
UniProt

4
CCDS

CCDS25712.1, CCDS88294.1

Ensembl

ENSMUSG00000039963 (Evidence)
NCBI Gene

207607

			Length	Strain/Species	Flank
genomic	ENSMUSG00000039963	Ensembl Gene Model \| MGI Sequence Detail	36667	C57BL/6J	± kb
transcript	ENSMUST00000236813	Ensembl \| MGI Sequence Detail	4769	Not Applicable
polypeptide	ENSMUSP00000158069	Ensembl \| MGI Sequence Detail	1262	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000031780 coiled-coil domain-containing protein 40

(term hierarchy)
InterPro Domains

IPR037386 Coiled-coil domain-containing protein 40
GlyGen

Q8BI79 1 site, 1 O-linked glycan (1 site)

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All nucleic 25

cDNA 25

Antibodies 1

Microarray probesets 2

Summaries

All 38

Developmental Gene Expression 3

Gene Ontology 10

Phenotypes 12
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:369747 Lin S, et al., Rbpms2 prevents major cardiac defects in cardiomyocyte-specific Rbpms-deficient mice. Dev Cell. 2025 Jun 24;

TSS for Ccdc40:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr106168	Chr11:119119918-119119957 (+)	540 bp
Tssr106169	Chr11:119149773-119149786 (+)	30,382 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)
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