PCDHB4 (protocadherin beta 4) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: PCDHB4 (protocadherin beta 4) Homo sapiens
Analyze
Symbol: PCDHB4
Name: protocadherin beta 4
RGD ID: 1312238
HGNC Page HGNC:8689
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in cell adhesion. Predicted to be located in plasma membrane.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: PCDH-beta-4; PCDH-BETA4; protocadherin beta-4
RGD Orthologs
Mouse
Rat
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385141,121,818 - 141,125,623 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5141,121,818 - 141,125,623 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,501,400 - 140,505,205 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,481,765 - 140,485,385 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,481,764 - 140,485,385NCBI
Celera5136,578,393 - 136,582,013 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,646,277 - 135,649,897 (+)NCBIHuRef
CHM1_15139,934,771 - 139,938,391 (+)NCBICHM1_1
T2T-CHM13v2.05141,647,136 - 141,650,941 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA,NAS)
plasma membrane  (IEA,TAS)
synapse  (IEA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Seizure  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10380929   PMID:10716726   PMID:10817752   PMID:10835267   PMID:11230163   PMID:11322959   PMID:12231349   PMID:12477932   PMID:15489334   PMID:16344560   PMID:18029348   PMID:21873635  
PMID:33961781  


Genomics

Comparative Map Data
PCDHB4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385141,121,818 - 141,125,623 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5141,121,818 - 141,125,623 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,501,400 - 140,505,205 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,481,765 - 140,485,385 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,481,764 - 140,485,385NCBI
Celera5136,578,393 - 136,582,013 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,646,277 - 135,649,897 (+)NCBIHuRef
CHM1_15139,934,771 - 139,938,391 (+)NCBICHM1_1
T2T-CHM13v2.05141,647,136 - 141,650,941 (+)NCBIT2T-CHM13v2.0
Pcdhb5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,453,434 - 37,456,966 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,453,434 - 37,456,968 (+)EnsemblGRCm39 Ensembl
GRCm381837,320,381 - 37,323,913 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,320,381 - 37,323,915 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,480,035 - 37,483,567 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,446,365 - 37,449,887 (+)NCBIMGSCv36mm8
MGSCv361837,507,497 - 37,511,019 (+)NCBIMGSCv36mm8
Celera1838,665,642 - 38,669,173 (+)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.47NCBI
Pcdhb5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,302,466 - 29,305,048 (+)NCBIGRCr8
mRatBN7.21829,024,315 - 29,032,183 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1829,028,382 - 29,053,259 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1829,155,586 - 29,158,168 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01829,917,648 - 29,920,230 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01829,252,881 - 29,255,463 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01830,398,113 - 30,400,695 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1830,398,113 - 30,400,695 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01830,105,642 - 30,108,224 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,127,192 - 30,129,774 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11830,154,026 - 30,156,418 (+)NCBI
Celera1828,731,022 - 28,733,604 (+)NCBICelera
Cytogenetic Map18p11NCBI
LOC103783391
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24136,364,588 - 136,382,380 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15134,514,756 - 134,521,932 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05136,484,686 - 136,489,194 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15142,598,785 - 142,601,642 (+)NCBIpanpan1.1PanPan1.1panPan2
LOC100855970
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1236,178,858 - 36,184,360 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha233,230,768 - 33,236,860 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0236,633,421 - 36,637,791 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl236,634,378 - 36,637,779 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1233,707,773 - 33,713,672 (+)NCBIUMICH_Zoey_3.1
UU_Cfam_GSD_1.0235,326,167 - 35,332,258 (+)NCBIUU_Cfam_GSD_1.0
LOC110259512
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.12142,816,658 - 142,822,048 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PCDHB4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12343,747,220 - 43,765,491 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603434,102,963 - 34,108,374 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in PCDHB4
63 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q23.3-33.2(chr5:130860928-155321811)x3 copy number gain See cases [RCV000051193] Chr5:130860928..155321811 [GRCh38]
Chr5:130196621..154701371 [GRCh37]
Chr5:130224520..154681564 [NCBI36]
Chr5:5q23.3-33.2
pathogenic
GRCh38/hg38 5q31.2-32(chr5:138871137-145812309)x1 copy number loss See cases [RCV000052142] Chr5:138871137..145812309 [GRCh38]
Chr5:138206826..145191872 [GRCh37]
Chr5:138234725..145172065 [NCBI36]
Chr5:5q31.2-32
pathogenic
GRCh38/hg38 5q21.3-33.2(chr5:106619588-156124387)x1 copy number loss See cases [RCV000053524] Chr5:106619588..156124387 [GRCh38]
Chr5:105955289..155551397 [GRCh37]
Chr5:105983188..155483975 [NCBI36]
Chr5:5q21.3-33.2
pathogenic
NM_018938.3(PCDHB4):c.258G>A (p.Arg86=) single nucleotide variant Malignant melanoma [RCV000066699] Chr5:141122256 [GRCh38]
Chr5:140501838 [GRCh37]
Chr5:140482022 [NCBI36]
Chr5:5q31.3
not provided
NM_018938.3(PCDHB4):c.259G>A (p.Glu87Lys) single nucleotide variant Malignant melanoma [RCV000066700] Chr5:141122257 [GRCh38]
Chr5:140501839 [GRCh37]
Chr5:140482023 [NCBI36]
Chr5:5q31.3
not provided
NM_018938.3(PCDHB4):c.581T>G (p.Val194Gly) single nucleotide variant Malignant melanoma [RCV000066701] Chr5:141122579 [GRCh38]
Chr5:140502161 [GRCh37]
Chr5:140482345 [NCBI36]
Chr5:5q31.3
not provided
NM_018938.3(PCDHB4):c.1830G>A (p.Glu610=) single nucleotide variant Malignant melanoma [RCV000066702] Chr5:141123828 [GRCh38]
Chr5:140503410 [GRCh37]
Chr5:140483594 [NCBI36]
Chr5:5q31.3
not provided
NM_018938.3(PCDHB4):c.2350G>A (p.Glu784Lys) single nucleotide variant Malignant melanoma [RCV000061143] Chr5:141124348 [GRCh38]
Chr5:140503930 [GRCh37]
Chr5:140484114 [NCBI36]
Chr5:5q31.3
not provided
GRCh38/hg38 5q31.3(chr5:140963199-142322798)x1 copy number loss See cases [RCV000136949] Chr5:140963199..142322798 [GRCh38]
Chr5:140453735..141702363 [GRCh37]
Chr5:140322968..141682547 [NCBI36]
Chr5:5q31.3
uncertain significance
GRCh38/hg38 5q23.3-33.2(chr5:129847794-153353546)x3 copy number gain See cases [RCV000138808] Chr5:129847794..153353546 [GRCh38]
Chr5:129183487..152733106 [GRCh37]
Chr5:129211386..152713299 [NCBI36]
Chr5:5q23.3-33.2
pathogenic
GRCh38/hg38 5q31.3-32(chr5:141089988-149530678)x3 copy number gain See cases [RCV000139504] Chr5:141089988..149530678 [GRCh38]
Chr5:140469572..148910241 [GRCh37]
Chr5:140449756..148890434 [NCBI36]
Chr5:5q31.3-32
pathogenic
GRCh38/hg38 5q31.2-31.3(chr5:138942857-144605017)x3 copy number gain See cases [RCV000142806] Chr5:138942857..144605017 [GRCh38]
Chr5:138278546..143984580 [GRCh37]
Chr5:138306445..143964773 [NCBI36]
Chr5:5q31.2-31.3
uncertain significance
NM_018938.4(PCDHB4):c.915del (p.Lys305fs) deletion Epilepsy [RCV002464133]|Seizure [RCV000162121]|not provided [RCV001589022] Chr5:141122905 [GRCh38]
Chr5:140502487 [GRCh37]
Chr5:5q31.3
likely pathogenic|uncertain significance|not provided
GRCh37/hg19 5q15-35.3(chr5:94844077-178830410)x3 copy number gain not provided [RCV000487658] Chr5:94844077..178830410 [GRCh37]
Chr5:5q15-35.3
likely benign
NC_000005.9:g.(?_86400000)_(154000000_?)del deletion Familial adenomatous polyposis 1 [RCV002231249]|Hereditary cancer-predisposing syndrome [RCV000554476] Chr5:86400000..154000000 [GRCh37]
Chr5:5q14.3-33.2
pathogenic
GRCh37/hg19 5q23.3-33.3(chr5:130125085-157574910)x3 copy number gain See cases [RCV000449349] Chr5:130125085..157574910 [GRCh37]
Chr5:5q23.3-33.3
pathogenic
GRCh37/hg19 5q21.3-35.3(chr5:106716357-180687338)x3 copy number gain See cases [RCV000448245] Chr5:106716357..180687338 [GRCh37]
Chr5:5q21.3-35.3
pathogenic
GRCh37/hg19 5p15.1-q35.2(chr5:17628741-176575720)x1 copy number loss See cases [RCV000511978] Chr5:17628741..176575720 [GRCh37]
Chr5:5p15.1-q35.2
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789)x3 copy number gain See cases [RCV000512039] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789) copy number gain See cases [RCV000510723] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
NM_018938.4(PCDHB4):c.1858A>G (p.Asn620Asp) single nucleotide variant Inborn genetic diseases [RCV003292151] Chr5:141123856 [GRCh38]
Chr5:140503438 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1698T>G (p.Asn566Lys) single nucleotide variant Inborn genetic diseases [RCV003255708] Chr5:141123696 [GRCh38]
Chr5:140503278 [GRCh37]
Chr5:5q31.3
uncertain significance
GRCh37/hg19 5q31.2-31.3(chr5:139147238-141540491)x1 copy number loss not provided [RCV000682600] Chr5:139147238..141540491 [GRCh37]
Chr5:5q31.2-31.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:25328-180693344)x3 copy number gain not provided [RCV000744323] Chr5:25328..180693344 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:13648-180905029)x3 copy number gain not provided [RCV000744317] Chr5:13648..180905029 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
NM_018938.4(PCDHB4):c.1998C>T (p.Ser666=) single nucleotide variant not provided [RCV000893207] Chr5:141123996 [GRCh38]
Chr5:140503578 [GRCh37]
Chr5:5q31.3
likely benign
Single allele deletion Neurodevelopmental disorder [RCV000787436] Chr5:14685137..149511942 [GRCh37]
Chr5:5p15.2-q32
uncertain significance
NM_018938.4(PCDHB4):c.1704C>T (p.Ser568=) single nucleotide variant not provided [RCV000905583] Chr5:141123702 [GRCh38]
Chr5:140503284 [GRCh37]
Chr5:5q31.3
likely benign
NM_018938.4(PCDHB4):c.1437G>A (p.Ser479=) single nucleotide variant not provided [RCV000971515] Chr5:141123435 [GRCh38]
Chr5:140503017 [GRCh37]
Chr5:5q31.3
benign
NM_018938.4(PCDHB4):c.1657A>G (p.Thr553Ala) single nucleotide variant not provided [RCV000948304] Chr5:141123655 [GRCh38]
Chr5:140503237 [GRCh37]
Chr5:5q31.3
benign
NM_018938.4(PCDHB4):c.1343C>G (p.Pro448Arg) single nucleotide variant Inborn genetic diseases [RCV003269759] Chr5:141123341 [GRCh38]
Chr5:140502923 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.503A>G (p.Lys168Arg) single nucleotide variant not provided [RCV000961654] Chr5:141122501 [GRCh38]
Chr5:140502083 [GRCh37]
Chr5:5q31.3
benign
NM_018938.4(PCDHB4):c.1572G>A (p.Gln524=) single nucleotide variant not provided [RCV000879081] Chr5:141123570 [GRCh38]
Chr5:140503152 [GRCh37]
Chr5:5q31.3
benign
NM_018938.4(PCDHB4):c.853G>C (p.Asp285His) single nucleotide variant not provided [RCV000958824] Chr5:141122851 [GRCh38]
Chr5:140502433 [GRCh37]
Chr5:5q31.3
benign
NM_018938.4(PCDHB4):c.1989T>C (p.Asp663=) single nucleotide variant not provided [RCV000893206] Chr5:141123987 [GRCh38]
Chr5:140503569 [GRCh37]
Chr5:5q31.3
benign
GRCh37/hg19 5q31.3-32(chr5:140424333-148985999)x3 copy number gain not provided [RCV000848228] Chr5:140424333..148985999 [GRCh37]
Chr5:5q31.3-32
uncertain significance
NM_018938.4(PCDHB4):c.1339G>C (p.Ala447Pro) single nucleotide variant not provided [RCV000974565] Chr5:141123337 [GRCh38]
Chr5:140502919 [GRCh37]
Chr5:5q31.3
benign
NM_018938.4(PCDHB4):c.1340C>A (p.Ala447Asp) single nucleotide variant not provided [RCV000974566] Chr5:141123338 [GRCh38]
Chr5:140502920 [GRCh37]
Chr5:5q31.3
benign
NM_018938.4(PCDHB4):c.1833T>C (p.Pro611=) single nucleotide variant not provided [RCV000974567] Chr5:141123831 [GRCh38]
Chr5:140503413 [GRCh37]
Chr5:5q31.3
likely benign
NM_018938.4(PCDHB4):c.1917C>G (p.Leu639=) single nucleotide variant not provided [RCV000930907] Chr5:141123915 [GRCh38]
Chr5:140503497 [GRCh37]
Chr5:5q31.3
likely benign
NM_018938.4(PCDHB4):c.630C>T (p.Thr210=) single nucleotide variant not provided [RCV000908045] Chr5:141122628 [GRCh38]
Chr5:140502210 [GRCh37]
Chr5:5q31.3
likely benign
NM_018938.4(PCDHB4):c.1451A>G (p.Gln484Arg) single nucleotide variant not provided [RCV000892269] Chr5:141123449 [GRCh38]
Chr5:140503031 [GRCh37]
Chr5:5q31.3
likely benign
NM_018938.4(PCDHB4):c.2052T>G (p.Ser684=) single nucleotide variant not provided [RCV000923688] Chr5:141124050 [GRCh38]
Chr5:140503632 [GRCh37]
Chr5:5q31.3
likely benign
NM_018938.4(PCDHB4):c.1153C>T (p.Pro385Ser) single nucleotide variant not provided [RCV000966350] Chr5:141123151 [GRCh38]
Chr5:140502733 [GRCh37]
Chr5:5q31.3
benign
NM_018938.4(PCDHB4):c.1521A>G (p.Ala507=) single nucleotide variant not provided [RCV000948709] Chr5:141123519 [GRCh38]
Chr5:140503101 [GRCh37]
Chr5:5q31.3
likely benign
NM_018938.4(PCDHB4):c.130G>T (p.Val44Leu) single nucleotide variant not provided [RCV000975081] Chr5:141122128 [GRCh38]
Chr5:140501710 [GRCh37]
Chr5:5q31.3
benign
NM_018938.4(PCDHB4):c.179C>T (p.Ser60Phe) single nucleotide variant not provided [RCV000956312] Chr5:141122177 [GRCh38]
Chr5:140501759 [GRCh37]
Chr5:5q31.3
benign
NM_018938.4(PCDHB4):c.764C>T (p.Pro255Leu) single nucleotide variant not provided [RCV001596716] Chr5:141122762 [GRCh38]
Chr5:140502344 [GRCh37]
Chr5:5q31.3
benign
NM_018938.4(PCDHB4):c.763C>T (p.Pro255Ser) single nucleotide variant not provided [RCV001647954] Chr5:141122761 [GRCh38]
Chr5:140502343 [GRCh37]
Chr5:5q31.3
benign
NC_000005.9:g.(?_136633338)_(140998481_?)dup duplication PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome [RCV001339088] Chr5:136633338..140998481 [GRCh37]
Chr5:5q31.2-31.3
uncertain significance
NM_018938.4(PCDHB4):c.597G>A (p.Leu199=) single nucleotide variant not provided [RCV001540054] Chr5:141122595 [GRCh38]
Chr5:140502177 [GRCh37]
Chr5:5q31.3
benign
GRCh37/hg19 5q31.2-31.3(chr5:139493717-140517454)x1 copy number loss PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome [RCV001801202] Chr5:139493717..140517454 [GRCh37]
Chr5:5q31.2-31.3
pathogenic
GRCh37/hg19 5q23.3-33.3(chr5:130125085-157574910) copy number gain not specified [RCV002053526] Chr5:130125085..157574910 [GRCh37]
Chr5:5q23.3-33.3
pathogenic
NM_018938.4(PCDHB4):c.2231T>A (p.Leu744Gln) single nucleotide variant Inborn genetic diseases [RCV002749665] Chr5:141124229 [GRCh38]
Chr5:140503811 [GRCh37]
Chr5:5q31.3
uncertain significance
GRCh37/hg19 5q31.3(chr5:140082762-140773954)x3 copy number gain not provided [RCV002474614] Chr5:140082762..140773954 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.2202T>G (p.His734Gln) single nucleotide variant Inborn genetic diseases [RCV002997458] Chr5:141124200 [GRCh38]
Chr5:140503782 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1507G>A (p.Val503Ile) single nucleotide variant Inborn genetic diseases [RCV002906222] Chr5:141123505 [GRCh38]
Chr5:140503087 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.2006A>G (p.Tyr669Cys) single nucleotide variant Inborn genetic diseases [RCV002845745] Chr5:141124004 [GRCh38]
Chr5:140503586 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1648G>A (p.Val550Met) single nucleotide variant Inborn genetic diseases [RCV002739963] Chr5:141123646 [GRCh38]
Chr5:140503228 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1796C>G (p.Ala599Gly) single nucleotide variant Inborn genetic diseases [RCV002691593] Chr5:141123794 [GRCh38]
Chr5:140503376 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1249A>T (p.Asn417Tyr) single nucleotide variant Inborn genetic diseases [RCV002757367] Chr5:141123247 [GRCh38]
Chr5:140502829 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1172T>C (p.Ile391Thr) single nucleotide variant Inborn genetic diseases [RCV002844447] Chr5:141123170 [GRCh38]
Chr5:140502752 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.803T>C (p.Ile268Thr) single nucleotide variant Inborn genetic diseases [RCV002869569] Chr5:141122801 [GRCh38]
Chr5:140502383 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.772T>C (p.Ser258Pro) single nucleotide variant Inborn genetic diseases [RCV002978517] Chr5:141122770 [GRCh38]
Chr5:140502352 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.2329G>C (p.Asp777His) single nucleotide variant Inborn genetic diseases [RCV002692315] Chr5:141124327 [GRCh38]
Chr5:140503909 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.931A>C (p.Ile311Leu) single nucleotide variant Inborn genetic diseases [RCV002844867] Chr5:141122929 [GRCh38]
Chr5:140502511 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1601A>G (p.Asp534Gly) single nucleotide variant Inborn genetic diseases [RCV002930226] Chr5:141123599 [GRCh38]
Chr5:140503181 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1890C>G (p.Ser630Arg) single nucleotide variant Inborn genetic diseases [RCV002665877] Chr5:141123888 [GRCh38]
Chr5:140503470 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1375G>C (p.Val459Leu) single nucleotide variant Inborn genetic diseases [RCV003003638] Chr5:141123373 [GRCh38]
Chr5:140502955 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.2367A>T (p.Arg789Ser) single nucleotide variant Inborn genetic diseases [RCV002786849] Chr5:141124365 [GRCh38]
Chr5:140503947 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.181C>G (p.Arg61Gly) single nucleotide variant Inborn genetic diseases [RCV002764124] Chr5:141122179 [GRCh38]
Chr5:140501761 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.932T>C (p.Ile311Thr) single nucleotide variant Inborn genetic diseases [RCV002954639] Chr5:141122930 [GRCh38]
Chr5:140502512 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1277G>A (p.Gly426Glu) single nucleotide variant Inborn genetic diseases [RCV002825916] Chr5:141123275 [GRCh38]
Chr5:140502857 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1374C>A (p.Phe458Leu) single nucleotide variant Inborn genetic diseases [RCV002804839] Chr5:141123372 [GRCh38]
Chr5:140502954 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.17G>A (p.Arg6Lys) single nucleotide variant Inborn genetic diseases [RCV002983487] Chr5:141122015 [GRCh38]
Chr5:140501597 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.586G>A (p.Asp196Asn) single nucleotide variant Inborn genetic diseases [RCV002960546] Chr5:141122584 [GRCh38]
Chr5:140502166 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1480G>A (p.Asp494Asn) single nucleotide variant Inborn genetic diseases [RCV003010716] Chr5:141123478 [GRCh38]
Chr5:140503060 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.634G>A (p.Val212Met) single nucleotide variant Inborn genetic diseases [RCV002987896] Chr5:141122632 [GRCh38]
Chr5:140502214 [GRCh37]
Chr5:5q31.3
likely benign
NM_018938.4(PCDHB4):c.1039A>T (p.Ile347Phe) single nucleotide variant Inborn genetic diseases [RCV002940705] Chr5:141123037 [GRCh38]
Chr5:140502619 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.932T>G (p.Ile311Ser) single nucleotide variant Inborn genetic diseases [RCV002878083] Chr5:141122930 [GRCh38]
Chr5:140502512 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.491A>G (p.Asn164Ser) single nucleotide variant Inborn genetic diseases [RCV002656100] Chr5:141122489 [GRCh38]
Chr5:140502071 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.652T>A (p.Ser218Thr) single nucleotide variant Inborn genetic diseases [RCV003202605] Chr5:141122650 [GRCh38]
Chr5:140502232 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1239C>A (p.Ser413Arg) single nucleotide variant Inborn genetic diseases [RCV003203102] Chr5:141123237 [GRCh38]
Chr5:140502819 [GRCh37]
Chr5:5q31.3
likely benign
NM_018938.4(PCDHB4):c.1517A>G (p.Asn506Ser) single nucleotide variant Inborn genetic diseases [RCV003189336] Chr5:141123515 [GRCh38]
Chr5:140503097 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.5A>G (p.Lys2Arg) single nucleotide variant Inborn genetic diseases [RCV003258168] Chr5:141122003 [GRCh38]
Chr5:140501585 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1548G>T (p.Arg516Ser) single nucleotide variant Inborn genetic diseases [RCV003173720] Chr5:141123546 [GRCh38]
Chr5:140503128 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1543C>T (p.Leu515Phe) single nucleotide variant Inborn genetic diseases [RCV003284956] Chr5:141123541 [GRCh38]
Chr5:140503123 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1187T>G (p.Leu396Trp) single nucleotide variant Inborn genetic diseases [RCV003362156] Chr5:141123185 [GRCh38]
Chr5:140502767 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1060T>A (p.Ser354Thr) single nucleotide variant Inborn genetic diseases [RCV003354098] Chr5:141123058 [GRCh38]
Chr5:140502640 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1061C>A (p.Ser354Tyr) single nucleotide variant Inborn genetic diseases [RCV003370717] Chr5:141123059 [GRCh38]
Chr5:140502641 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018938.4(PCDHB4):c.1079_1080del (p.Pro360fs) deletion not provided [RCV003429823] Chr5:141123077..141123078 [GRCh38]
Chr5:140502659..140502660 [GRCh37]
Chr5:5q31.3
benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:429
Count of miRNA genes:304
Interacting mature miRNAs:324
Transcripts:ENST00000194152
Prediction methods:Miranda
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region
G65651  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375140,504,545 - 140,504,968UniSTSGRCh37
Build 365140,484,729 - 140,485,152RGDNCBI36
Celera5136,581,357 - 136,581,780RGD
Cytogenetic Map5q31UniSTS
HuRef5135,649,241 - 135,649,664UniSTS
RH78811  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375140,505,017 - 140,505,141UniSTSGRCh37
Build 365140,485,201 - 140,485,325RGDNCBI36
Celera5136,581,829 - 136,581,953RGD
Cytogenetic Map5q31UniSTS
HuRef5135,649,713 - 135,649,837UniSTS
GeneMap99-GB4 RH Map5531.42UniSTS
NCBI RH Map5889.1UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 4 307 9 2 1 2 352 2 329 24 104 20 25 325
Low 2202 1853 1299 262 416 103 3860 2074 3376 313 1241 1474 164 1 1179 2426 2 2
Below cutoff 155 437 397 341 575 341 135 107 26 70 76 88 6 37 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_000017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NG_050761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_018938 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC005754 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC244517 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF152497 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF217754 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK308946 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK313640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AW135510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC098139 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC098284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC098346 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC099725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA231000 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA409037 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENST00000194152   ⟹   ENSP00000194152
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5141,121,818 - 141,125,623 (+)Ensembl
RefSeq Acc Id: ENST00000623478
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5141,121,818 - 141,124,147 (+)Ensembl
RefSeq Acc Id: NM_018938   ⟹   NP_061761
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,121,818 - 141,125,623 (+)NCBI
GRCh375140,501,581 - 140,505,201 (+)RGD
Build 365140,481,765 - 140,485,385 (+)NCBI Archive
Celera5136,578,393 - 136,582,013 (+)RGD
HuRef5135,646,028 - 135,649,901 (+)NCBI
CHM1_15139,934,522 - 139,938,395 (+)NCBI
T2T-CHM13v2.05141,647,136 - 141,650,941 (+)NCBI
Sequence:
RefSeq Acc Id: NP_061761   ⟸   NM_018938
- Peptide Label: precursor
- UniProtKB: Q4V761 (UniProtKB/Swiss-Prot),   Q9Y5E5 (UniProtKB/Swiss-Prot),   B2R951 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000194152   ⟸   ENST00000194152
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9Y5E5-F1-model_v2 AlphaFold Q9Y5E5 1-795 view protein structure

Promoters
RGD ID:6870936
Promoter ID:EPDNEW_H8632
Type:initiation region
Name:PCDHB4_1
Description:protocadherin beta 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,121,818 - 141,121,878EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:8689 AgrOrtholog
COSMIC PCDHB4 COSMIC
Ensembl Genes ENSG00000081818 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSG00000291676 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000194152 ENTREZGENE
  ENST00000194152.4 UniProtKB/Swiss-Prot
  ENST00000708352.1 UniProtKB/Swiss-Prot
Gene3D-CATH Cadherins UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000081818 GTEx
  ENSG00000291676 GTEx
HGNC ID HGNC:8689 ENTREZGENE
Human Proteome Map PCDHB4 Human Proteome Map
InterPro Cadherin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:56131 UniProtKB/Swiss-Prot
NCBI Gene 56131 ENTREZGENE
OMIM 606330 OMIM
PANTHER CADHERIN-87A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTOCADHERIN BETA-4 UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
Pfam Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_C_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA33038 PharmGKB
PRINTS CADHERIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Cadherin-like UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt B2R951 ENTREZGENE, UniProtKB/TrEMBL
  PCDB4_HUMAN UniProtKB/Swiss-Prot
  Q4V761 ENTREZGENE
  Q9Y5E5 ENTREZGENE
UniProt Secondary Q4V761 UniProtKB/Swiss-Prot