Chd7 MGI Mouse Gene Detail - MGI:2444748 - chromodomain helicase DNA binding protein 7

Symbol

Chd7
Name

chromodomain helicase DNA binding protein 7
Synonyms

A730019I05Rik, Cycn, Cyn, Dz, Edy, Flo, GENA 47, Gena 52, GENA 60, Lda, Mt, Obt, Todo, WBE1, Whi

Feature Type

protein coding gene
IDs

MGI:2444748
NCBI Gene: 320790
Alliance

gene page
Transcription Start Sites

37 TSS

Sequence Map

Chr4:8690406-8867659 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 4, 3.68 cM
Mapping Data

11 experiments

SNPs within 2kb

4642 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2444748	protein coding gene	Chr4:8690345-8868449 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0028040	protein coding gene	Chr4:5274100-5457337 (+)
A/J	MGP_AJ_G0027998	protein coding gene	Chr4:5164481-5345051 (+)
AKR/J	MGP_AKRJ_G0027964	protein coding gene	Chr4:5207076-5387587 (+)
BALB/cJ	MGP_BALBcJ_G0028010	protein coding gene	Chr4:5150351-5328217 (+)
C3H/HeJ	MGP_C3HHeJ_G0027740	protein coding gene	Chr4:5375729-5559400 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0028453	protein coding gene	Chr4:5572377-5757166 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0025797	protein coding gene	Chr4:4856621-5033485 (+)
CAST/EiJ	MGP_CASTEiJ_G0027194	protein coding gene	Chr4:5211917-5394660 (+)
CBA/J	MGP_CBAJ_G0027715	protein coding gene	Chr4:5650822-5838013 (+)
DBA/2J	MGP_DBA2J_G0027855	protein coding gene	Chr4:5134271-5311757 (+)
FVB/NJ	MGP_FVBNJ_G0027822	protein coding gene	Chr4:5003214-5183734 (+)
LP/J	MGP_LPJ_G0027966	protein coding gene	Chr4:5285992-5469312 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0027855	protein coding gene	Chr4:5887680-6072916 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0028512	protein coding gene	Chr4:5202648-5384159 (+)
PWK/PhJ	MGP_PWKPhJ_G0026915	protein coding gene	Chr4:5134183-5316046 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0026745	protein coding gene	Chr4:5154346-5334205 (+)
WSB/EiJ	MGP_WSBEiJ_G0027273	protein coding gene	Chr4:5297957-5498628 (+)

Human Ortholog

CHD7, chromodomain helicase DNA binding protein 7

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CHD7, chromodomain helicase DNA binding protein 7
Synonyms

CRG, HH5, IS3, KAL5
Links

HGNC:20626

NCBI Gene ID: 55636

neXtProt AC: NX_Q9P2D1

UniProt: Q9P2D1
Chr Location

8q12.2

MGI Vertebrate Homology

Chd7 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: CHD7
Gene Tree

Chd7

Diseases

1 with Chd7 mouse models; 2 with human CHD7 associations

Human Disease

Mouse Models

CHARGE syndrome

IDs

View 20 models

hypogonadotropic hypogonadism 5 with or without anosmia

IDs

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

Mutations/Alleles

9 with disease annotations

References

16 with disease annotations

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Phenotype Summary

359 phenotypes from 22 alleles in 50 genetic backgrounds
42 phenotypes from multigenic genotypes
10 images
73 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

55
Chemically induced (ENU)

12
Endonuclease-mediated

7
Gene trapped

25
Spontaneous

1
Targeted

10
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

138 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Heterozygotes for mutations of this gene show a variety of combinations of hyperactivity, circling, head-bobbing, semicircular canal defects, hearing loss, reduced size, tail-kink and reproductive system anomalies. Heterozygotes for a null allele show mild cerebellar hypoplasia and distinct cerebellar foliation anomalies.

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All GO Annotations

91
GO References

16

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	non-membrane-bounded 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

1145
Tissues

215
cDNA Data

18
Literature Summary

41

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

GEISHA CHD7

Xenbase chd7

ZFIN chd7

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All Sequences

69
RefSeq

13
UniProt

5
CCDS

CCDS38689.1

Ensembl

ENSMUSG00000041235 (Evidence)
NCBI Gene

320790

			Length	Strain/Species	Flank
genomic	ENSMUSG00000041235	Ensembl Gene Model \| MGI Sequence Detail	177254	C57BL/6J	± kb
transcript	ENSMUST00000051558	Ensembl \| MGI Sequence Detail	10216	Not Applicable
polypeptide	ENSMUSP00000059079	Ensembl \| MGI Sequence Detail	2986	Not Applicable

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UniProt

5 Sequences
Protein Ontology

PR:000005413 chromodomain-helicase-DNA-binding protein 7

(term hierarchy)
EC

3.6.4.12
InterPro Domains

IPR006576 BRK domain

IPR037259 BRK domain superfamily

IPR000953 Chromo/chromo shadow domain

IPR023780 Chromo domain

IPR051493 Chromodomain-helicase-DNA-binding

IPR016197 Chromo-like domain superfamily

IPR001650 Helicase, C-terminal domain-like

IPR014001 Helicase superfamily 1/2, ATP-binding domain

IPR027417 P-loop containing nucleoside triphosphate hydrolase

IPR038718 SNF2-like, N-terminal domain superfamily

IPR000330 SNF2, N-terminal

IPR049730 SNF2/RAD5-like, C-terminal helicase domain

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All nucleic 28

cDNA 18

Primer pair 8

Other 2

Microarray probesets 35

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MGI:1861982, MGI:1861985, MGI:1861987, MGI:1861988, MGI:1862038, MGI:1890591, MGI:1890592, MGI:2662565, MGI:2662566

Summaries

All 118

Developmental Gene Expression 41

Diseases 16

Gene Ontology 16

Phenotypes 73
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:353363 Gao J, et al., CHD7 and SOX2 act in a common gene regulatory network during mammalian semicircular canal and cochlear development. Proc Natl Acad Sci U S A. 2024 Mar 5;121(10):e2311720121

TSS for Chd7:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr36414	Chr4:8690399-8690453 (+)	20 bp
Tssr36415	Chr4:8690537-8690583 (+)	154 bp
Tssr36416	Chr4:8691303-8691380 (+)	936 bp
Tssr36417	Chr4:8711764-8711767 (+)	21,360 bp
Tssr36418	Chr4:8731997-8732000 (+)	41,593 bp
Tssr36419	Chr4:8735931-8735942 (+)	45,531 bp
Tssr36420	Chr4:8735946-8735963 (+)	45,549 bp
Tssr36421	Chr4:8735969-8736085 (+)	45,621 bp
Tssr1115	Chr4:8736088-8736099 (+)	45,688 bp
Tssr36422	Chr4:8752330-8752351 (+)	61,935 bp
Tssr36423	Chr4:8785543-8785550 (+)	95,141 bp
Tssr36424	Chr4:8785651-8785688 (+)	95,264 bp
Tssr36425	Chr4:8800212-8800237 (+)	109,819 bp
Tssr36426	Chr4:8803427-8803441 (+)	113,028 bp
Tssr36427	Chr4:8806245-8806252 (+)	115,843 bp
Tssr36428	Chr4:8811279-8811290 (+)	120,879 bp
Tssr36429	Chr4:8811323-8811339 (+)	120,925 bp
Tssr36430	Chr4:8811341-8811342 (+)	120,936 bp
Tssr36431	Chr4:8811346-8811357 (+)	120,946 bp
Tssr36432	Chr4:8811363-8811377 (+)	120,964 bp
Tssr36433	Chr4:8811421-8811440 (+)	121,025 bp
Tssr36434	Chr4:8821771-8821780 (+)	131,370 bp
Tssr36435	Chr4:8821783-8821802 (+)	131,387 bp
Tssr1116	Chr4:8822135-8822139 (+)	131,731 bp
Tssr36436	Chr4:8822782-8822804 (+)	132,387 bp
Tssr36437	Chr4:8822809-8822818 (+)	132,408 bp
Tssr36438	Chr4:8837710-8837722 (+)	147,310 bp
Tssr36439	Chr4:8837728-8837754 (+)	147,335 bp
Tssr36440	Chr4:8837825-8837836 (+)	147,425 bp
Tssr36441	Chr4:8838989-8839003 (+)	148,590 bp
Tssr36442	Chr4:8840334-8840347 (+)	149,935 bp
Tssr36443	Chr4:8840365-8840391 (+)	149,972 bp
Tssr36444	Chr4:8840483-8840493 (+)	150,082 bp
Tssr36445	Chr4:8842377-8842381 (+)	151,973 bp
Tssr36446	Chr4:8842711-8842714 (+)	152,307 bp
Tssr1117	Chr4:8843035-8843038 (+)	152,631 bp
Tssr36447	Chr4:8854198-8854204 (+)	163,795 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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