Pcdha9 MGI Mouse Gene Detail - MGI:2447322

Symbol

Pcdha9
Name

protocadherin alpha 9

Feature Type

protein coding gene
IDs

MGI:2447322
NCBI Gene: 192161
Member of

Pcdha cluster
Alliance

gene page
Transcription Start Sites

1 TSS

Sequence Map

Chr18:37130933-37320710 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 18, 19.46 cM
Mapping Data

2 experiments

SNPs within 2kb

4901 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2447322	protein coding gene	Chr18:37130933-37320710 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0024304	protein coding gene	Chr18:35403981-35583235 (+)
A/J	MGP_AJ_G0024271	protein coding gene	Chr18:34173525-34357515 (+)
AKR/J	MGP_AKRJ_G0024239	protein coding gene	Chr18:35136997-35313391 (+)
BALB/cJ	MGP_BALBcJ_G0024270	protein coding gene	Chr18:34224888-34406362 (+)
C3H/HeJ	MGP_C3HHeJ_G0024037	protein coding gene	Chr18:35189302-35358175 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0024712	protein coding gene	Chr18:36669229-36867648 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022151	protein coding gene	Chr18:34262022-34436126 (+)
CAST/EiJ	MGP_CASTEiJ_G0023512	protein coding gene	Chr18:35189716-35356123 (+)
CBA/J	MGP_CBAJ_G0024006	protein coding gene	Chr18:37745369-37945878 (+)
DBA/2J	MGP_DBA2J_G0024137	protein coding gene	Chr18:33793575-33963728 (+)
FVB/NJ	MGP_FVBNJ_G0024103	protein coding gene	Chr18:33502770-33689539 (+)
LP/J	MGP_LPJ_G0024220	protein coding gene	Chr18:35476646-35676922 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0024132	protein coding gene	Chr18:38998371-39218915 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0024761	protein coding gene	Chr18:35003564-35180644 (+)
PWK/PhJ	MGP_PWKPhJ_G0023257	protein coding gene	Chr18:34035916-34203479 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0023061	protein coding gene	Chr18:35253730-35441752 (+)
WSB/EiJ	MGP_WSBEiJ_G0023575	protein coding gene	Chr18:34907069-35081773 (+)

Human Ortholog

PCDHA10, protocadherin alpha 10

Vertebrate Orthologs

10

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

PCDHA10, protocadherin alpha 10
Synonyms

CNR8, CNRN8, CNRS8, CRNR8, PCDH-ALPHA10
Links

HGNC:8664

NCBI Gene ID: 56139

neXtProt AC: NX_Q9Y5I2

UniProt: Q9Y5I2
Chr Location

5q31.3; chr5:140855883-141012347 (+) GRCh38

MGI Vertebrate Homology

Pcdha9 stringent orthology
1 human;1 mouse;9 zebrafish
HCOP

vertebrate homology predictions: PCDHA10
Gene Tree

Pcdha9

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Mutations/Alleles

1 with disease annotations

References

1 with disease annotations

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Phenotype Summary

4 phenotypes from 1 allele in 1 genetic background
6 phenotypes from multigenic genotypes
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	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

8
Chemically induced (ENU)

1
Endonuclease-mediated

3
Targeted

4
Genomic Mutations

5 involving Pcdha9
Incidental Mutations

APF , CvDC
Find Mice (IMSR)

45 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for an ENU-induced mutation exhibit cardiac hypertrophy, aorta hypoplasia and stenosis, and bicuspid aortic valve.

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All GO Annotations

22
GO References

6

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

735
Tissues

23
cDNA Data

5
Literature Summary

10

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

28
RefSeq

2
UniProt

2
CCDS

CCDS37777.1

Ensembl

ENSMUSG00000103770 (Evidence)
NCBI Gene

192161

			Length	Strain/Species	Flank
genomic	192161	NCBI Gene Model \| MGI Sequence Detail	189778	C57BL/6J	± kb
transcript	NM_138661	RefSeq \| MGI Sequence Detail	5341	Not Specified
polypeptide	Q91Y11	UniProt \| EBI \| MGI Sequence Detail	979	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000012357 protocadherin alpha-10

(term hierarchy)
InterPro Domains

IPR020894 Cadherin conserved site

IPR031904 Cadherin, C-terminal catenin-binding domain

IPR002126 Cadherin-like

IPR015919 Cadherin-like superfamily

IPR013164 Cadherin, N-terminal

IPR050174 Protocadherin/Cadherin-related Cell Adhesion
GlyGen

Q91Y11 4 sites, 2 N-linked glycans (2 sites)

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All nucleic 9

cDNA 5

Primer pair 3

Other 1

Microarray probesets 1

Summaries

All 38

Developmental Gene Expression 10

Diseases 1

Gene Ontology 6

Phenotypes 11
Earliest

J:48282 Kohmura N, et al., Diversity revealed by a novel family of cadherins expressed in neurons at a synaptic complex. Neuron. 1998 Jun;20(6):1137-51
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Pcdha9:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr5284	Chr18:37130860-37130878 (+)	-64 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