Pcdh1 MGI Mouse Gene Detail - MGI:104692

Symbol

Pcdh1
Name

protocadherin 1
Synonyms

2010005A06Rik

Feature Type

protein coding gene
IDs

MGI:104692
NCBI Gene: 75599
Alliance

genome feature page
Transcription Start Sites

10 TSS

Sequence Map

Chr18:38318967-38345023 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 18, 20.08 cM
Mapping Data

3 experiments

SNPs within 2kb

409 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_104692	protein coding gene	Chr18:38318967-38345106 (-)
129S1/SvImJ	ENSMUSG00200041027	protein coding gene	Chr18:35319594-35341274 (-)
A/J	ENSMUSG00195032333	protein coding gene	Chr18:35472175-35493864 (-)
AKR/J	ENSMUSG00220016205	protein coding gene	Chr18:35440239-35461920 (-)
BALB/cJ	ENSMUSG00180018124	protein coding gene	Chr18:35921810-35943490 (-)
C3H/HeJ	ENSMUSG00175037370	protein coding gene	Chr18:35434761-35456429 (-)
C57BL/6NJ	ENSMUSG00215010586	protein coding gene	Chr18:35191563-35213228 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022207	protein coding gene	Chr18:35377106-35403325 (-)
CAST/EiJ	ENSTCUG00005020461	protein coding gene	Chr18:35051269-35072976 (-)
CBA/J	ENSMUSG00210020176	protein coding gene	Chr18:35463832-35485516 (-)
DBA/2J	ENSMUSG00185017997	protein coding gene	Chr18:35398427-35420113 (-)
FVB/NJ	ENSMUSG00205018635	protein coding gene	Chr18:35098518-35120198 (-)
JF1/MsJ	ENSUMUG00000022248	protein coding gene	Chr18:35529334-35551095 (-)
LP/J	ENSMUSG00230045478	protein coding gene	Chr18:37513720-37535402 (-)
NOD/ShiLtJ	ENSMUSG00190020563	protein coding gene	Chr18:35183102-35204775 (-)
NZO/HlLtJ	ENSMUSG00225043429	protein coding gene	Chr18:37420611-37442285 (-)
PWK/PhJ	ENSLUMG00010011102	protein coding gene	Chr18:35675832-35697598 (-)
SPRET/EiJ	ENSMSPG00010018816	protein coding gene	Chr18:35710410-35732103 (-)
WSB/EiJ	ENSIUOG00005007214	protein coding gene	Chr18:35178084-35199764 (-)

Human Ortholog

PCDH1, protocadherin 1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

PCDH1, protocadherin 1
Synonyms

PC42, PCDH42
Links

HGNC:8655

NCBI Gene ID: 5097

UniProt: Q08174
Chr Location

5q31.3; chr5:141853090-141879246 (-) GRCh38

MGI Vertebrate Homology

Pcdh1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: PCDH1
Gene Tree

Pcdh1

Diseases

3 with human PCDH1 associations

				Human Disease	Mouse Models
				asthma IDs asthma DOID:2841 DOID:12703 DOID:13829 DOID:13830 DOID:2840 DOID:5783 ICD10CM:J45 ICD9CM:493 ICD9CM:493.9 KEGG:05310 MESH:D001249 NCI:C28397 OMIM:600807 UMLS_CUI:C0004096
				atopic dermatitis IDs atopic dermatitis DOID:3310 EFO:0000274 ICD10CM:L20 MESH:D003876 NCI:C211594 OMIM:603165 OMIM:PS603165 UMLS_CUI:C0011615
				intrinsic asthma IDs intrinsic asthma DOID:9360 DOID:9361 DOID:9363 ICD10CM:J45 ICD9CM:493.1 UMLS_CUI:C0155880

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

less

Phenotype Summary

1 phenotype from 1 allele in 1 genetic background
10 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
Endonuclease-mediated

4
Gene trapped

2
Targeted

2
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

54 strains or lines available

less

All GO Annotations

14
GO References

7

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

738
Tissues

112
cDNA Data

5
Literature Summary

8

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA PCDH1

Xenbase pcdh1

ZFIN pcdh1b

less

All Sequences

70
RefSeq

14
UniProt

12
CCDS

CCDS29197.1

Ensembl

ENSMUSG00000051375 (Evidence)
NCBI Gene

75599

			Length	Strain/Species	Flank
genomic	75599	NCBI Gene Model \| MGI Sequence Detail	26057	C57BL/6J	± kb
transcript	NM_001403795	RefSeq \| MGI Sequence Detail	7490	ZRU/MplStud
polypeptide	NP_001390724	RefSeq \| MGI Sequence Detail	1216	ZRU/MplStud

less

UniProt

12 Sequences
InterPro Domains

IPR020894 Cadherin conserved site

IPR002126 Cadherin-like

IPR015919 Cadherin-like superfamily

IPR013164 Cadherin, N-terminal

IPR013585 Protocadherin

IPR050174 Protocadherin/Cadherin-related Cell Adhesion
GlyGen

Q8CFX3 6 sites, 10 N-linked glycans (6 sites)

less

All nucleic 8

cDNA 5

Primer pair 2

Other 1

Microarray probesets 4

less

MGD-MRK-27055, MGI:1922849, MGI:2147243

Summaries

All 45

Developmental Gene Expression 8

Gene Ontology 7

Phenotypes 10
Earliest

J:12571 Sano K, et al., Protocadherins: a large family of cadherin-related molecules in central nervous system. EMBO J. 1993 Jun;12(6):2249-56
Latest

J:372013 Mincheva-Tasheva S, et al., Mapping combinatorial expression of non-clustered protocadherins in the developing brain identifies novel PCDH19-mediated cell adhesion properties. Open Biol. 2024 Apr;14(4):230383

TSS for Pcdh1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr153025	Chr18:38345010-38345048 (-)	-6 bp
Tssr153024	Chr18:38342820-38342839 (-)	2,193 bp
Tssr153023	Chr18:38342786-38342800 (-)	2,230 bp
Tssr153022	Chr18:38342729-38342781 (-)	2,268 bp
Tssr153021	Chr18:38342695-38342723 (-)	2,314 bp
Tssr153020	Chr18:38336895-38336904 (-)	8,123 bp
Tssr153019	Chr18:38336886-38336889 (-)	8,135 bp
Tssr153018	Chr18:38336851-38336881 (-)	8,157 bp
Tssr153017	Chr18:38336837-38336848 (-)	8,180 bp
Tssr153016	Chr18:38325174-38325181 (-)	19,845 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 09/08/2026 MGI 6.24