PCDHB6 (protocadherin beta 6) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: PCDHB6 (protocadherin beta 6) Homo sapiens
Analyze
Symbol: PCDHB6
Name: protocadherin beta 6
RGD ID: 1321102
HGNC Page HGNC:8691
Description: Predicted to enable calcium ion binding activity and identical protein binding activity. Predicted to be involved in cell-cell recognition and homophilic cell adhesion via plasma membrane adhesion molecules. Predicted to be located in plasma membrane.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: PCDH-beta-6; PCDH-BETA6; protocadherin beta-6
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
GRCh385141,150,057 - 141,153,287 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5141,150,057 - 141,153,287 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,529,638 - 140,532,868 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,510,023 - 140,513,052 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,510,022 - 140,513,052NCBI
Celera5136,606,652 - 136,609,682 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,674,536 - 135,677,566 (+)NCBIHuRef
CHM1_15139,963,030 - 139,966,059 (+)NCBICHM1_1
T2T-CHM13v2.05141,675,376 - 141,678,606 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

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

Molecular Function

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:16344560   PMID:21873635   PMID:28514442   PMID:33961781  


Genomics

Comparative Map Data
PCDHB6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385141,150,057 - 141,153,287 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5141,150,057 - 141,153,287 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,529,638 - 140,532,868 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,510,023 - 140,513,052 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,510,022 - 140,513,052NCBI
Celera5136,606,652 - 136,609,682 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,674,536 - 135,677,566 (+)NCBIHuRef
CHM1_15139,963,030 - 139,966,059 (+)NCBICHM1_1
T2T-CHM13v2.05141,675,376 - 141,678,606 (+)NCBIT2T-CHM13v2.0
Pcdhb13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,575,570 - 37,579,262 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,575,553 - 37,579,262 (+)EnsemblGRCm39 Ensembl
GRCm381837,442,517 - 37,446,209 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,442,500 - 37,446,209 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,602,171 - 37,605,863 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,568,545 - 37,570,935 (+)NCBIMGSCv36mm8
Celera1838,793,815 - 38,797,507 (+)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.49NCBI
Pcdhb6l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,420,029 - 29,423,883 (+)NCBIGRCr8
mRatBN7.21829,146,017 - 29,149,871 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1829,146,313 - 29,148,703 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01830,512,507 - 30,518,524 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1830,515,962 - 30,518,352 (+)EnsemblRnor6.0rn6Rnor6.0
Celera1828,838,655 - 28,844,672 (+)NCBICelera
Cytogenetic Map18p11NCBI
LOC100988105
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24136,395,123 - 136,409,829 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15134,534,672 - 134,549,381 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05136,509,096 - 136,516,640 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15142,626,989 - 142,630,240 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5142,627,220 - 142,629,604 (+)Ensemblpanpan1.1panPan2
LOC487173
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1236,207,400 - 36,211,372 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl236,208,071 - 36,210,518 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha233,259,301 - 33,263,285 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0236,662,060 - 36,666,037 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl236,662,791 - 36,665,094 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1233,736,104 - 33,740,078 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0234,547,077 - 34,551,044 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0235,354,707 - 35,358,681 (+)NCBIUU_Cfam_GSD_1.0
PCDHB6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.12142,868,141 - 142,872,850 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22148,941,953 - 148,949,528 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PCDHB6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12343,774,538 - 43,785,507 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603434,075,538 - 34,083,002 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in PCDHB6
48 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_018939.3(PCDHB6):c.777G>A (p.Leu259=) single nucleotide variant Malignant melanoma [RCV000066706] Chr5:141151034 [GRCh38]
Chr5:140530615 [GRCh37]
Chr5:140510799 [NCBI36]
Chr5:5q31.3
not provided
NM_018939.3(PCDHB6):c.778G>A (p.Val260Ile) single nucleotide variant Malignant melanoma [RCV000066707] Chr5:141151035 [GRCh38]
Chr5:140530616 [GRCh37]
Chr5:140510800 [NCBI36]
Chr5:5q31.3
not provided
NM_018939.3(PCDHB6):c.2352C>T (p.Thr784=) single nucleotide variant Malignant melanoma [RCV000061147] Chr5:141152609 [GRCh38]
Chr5:140532190 [GRCh37]
Chr5:140512374 [NCBI36]
Chr5:5q31.3
not provided
NR_001280.1:n.403G>A single nucleotide variant Malignant melanoma [RCV000066708] Chr5:141156401 [GRCh38]
Chr5:140535982 [GRCh37]
Chr5:140516166 [NCBI36]
Chr5:5q31.3
not provided
NR_001280.1:n.429C>T single nucleotide variant Malignant melanoma [RCV000066709] Chr5:141156427 [GRCh38]
Chr5:140536008 [GRCh37]
Chr5:140516192 [NCBI36]
Chr5:5q31.3
not provided
NR_001280.1:n.1127G>A single nucleotide variant Malignant melanoma [RCV000066710] Chr5:141157125 [GRCh38]
Chr5:140536706 [GRCh37]
Chr5:140516890 [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
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_018939.4(PCDHB6):c.2215G>C (p.Gly739Arg) single nucleotide variant Inborn genetic diseases [RCV003240654] Chr5:141152472 [GRCh38]
Chr5:140532053 [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
Single allele deletion Neurodevelopmental disorder [RCV000787436] Chr5:14685137..149511942 [GRCh37]
Chr5:5p15.2-q32
uncertain significance
NM_018939.4(PCDHB6):c.2098C>T (p.Leu700Phe) single nucleotide variant Inborn genetic diseases [RCV003248364] Chr5:141152355 [GRCh38]
Chr5:140531936 [GRCh37]
Chr5:5q31.3
uncertain significance
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_018939.4(PCDHB6):c.1048T>C (p.Phe350Leu) single nucleotide variant Inborn genetic diseases [RCV003246083] Chr5:141151305 [GRCh38]
Chr5:140530886 [GRCh37]
Chr5:5q31.3
likely benign
NM_018939.4(PCDHB6):c.1613C>G (p.Ala538Gly) single nucleotide variant Inborn genetic diseases [RCV003274789] Chr5:141151870 [GRCh38]
Chr5:140531451 [GRCh37]
Chr5:5q31.3
uncertain significance
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
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_018939.4(PCDHB6):c.2299C>A (p.Pro767Thr) single nucleotide variant Inborn genetic diseases [RCV003254096] Chr5:141152556 [GRCh38]
Chr5:140532137 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.410T>C (p.Met137Thr) single nucleotide variant Inborn genetic diseases [RCV003297772] Chr5:141150667 [GRCh38]
Chr5:140530248 [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_018939.4(PCDHB6):c.676G>A (p.Glu226Lys) single nucleotide variant Inborn genetic diseases [RCV002817411] Chr5:141150933 [GRCh38]
Chr5:140530514 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1927A>G (p.Lys643Glu) single nucleotide variant Inborn genetic diseases [RCV002879463] Chr5:141152184 [GRCh38]
Chr5:140531765 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.169G>A (p.Glu57Lys) single nucleotide variant Inborn genetic diseases [RCV002818952] Chr5:141150426 [GRCh38]
Chr5:140530007 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.500A>G (p.Gln167Arg) single nucleotide variant Inborn genetic diseases [RCV002882592] Chr5:141150757 [GRCh38]
Chr5:140530338 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.704A>G (p.Asn235Ser) single nucleotide variant Inborn genetic diseases [RCV002981244] Chr5:141150961 [GRCh38]
Chr5:140530542 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1571C>A (p.Ser524Tyr) single nucleotide variant Inborn genetic diseases [RCV002977413] Chr5:141151828 [GRCh38]
Chr5:140531409 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1848G>C (p.Trp616Cys) single nucleotide variant Inborn genetic diseases [RCV002977617] Chr5:141152105 [GRCh38]
Chr5:140531686 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1624G>C (p.Glu542Gln) single nucleotide variant Inborn genetic diseases [RCV002692014] Chr5:141151881 [GRCh38]
Chr5:140531462 [GRCh37]
Chr5:5q31.3
likely benign
NM_018939.4(PCDHB6):c.1771G>A (p.Asp591Asn) single nucleotide variant Inborn genetic diseases [RCV002799627] Chr5:141152028 [GRCh38]
Chr5:140531609 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1039A>T (p.Met347Leu) single nucleotide variant Inborn genetic diseases [RCV002977600] Chr5:141151296 [GRCh38]
Chr5:140530877 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1530C>A (p.His510Gln) single nucleotide variant Inborn genetic diseases [RCV002758404] Chr5:141151787 [GRCh38]
Chr5:140531368 [GRCh37]
Chr5:5q31.3
likely benign
NM_018939.4(PCDHB6):c.662G>T (p.Arg221Leu) single nucleotide variant Inborn genetic diseases [RCV002978218] Chr5:141150919 [GRCh38]
Chr5:140530500 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.41C>T (p.Ala14Val) single nucleotide variant Inborn genetic diseases [RCV002892010] Chr5:141150298 [GRCh38]
Chr5:140529879 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.649G>C (p.Gly217Arg) single nucleotide variant Inborn genetic diseases [RCV002955319] Chr5:141150906 [GRCh38]
Chr5:140530487 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1813C>A (p.Leu605Ile) single nucleotide variant Inborn genetic diseases [RCV002744014] Chr5:141152070 [GRCh38]
Chr5:140531651 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.179C>T (p.Ser60Leu) single nucleotide variant Inborn genetic diseases [RCV003004783] Chr5:141150436 [GRCh38]
Chr5:140530017 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.2201T>A (p.Leu734Gln) single nucleotide variant Inborn genetic diseases [RCV002850356] Chr5:141152458 [GRCh38]
Chr5:140532039 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1599C>A (p.Asp533Glu) single nucleotide variant Inborn genetic diseases [RCV002955443] Chr5:141151856 [GRCh38]
Chr5:140531437 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1856A>T (p.Asn619Ile) single nucleotide variant Inborn genetic diseases [RCV002930951] Chr5:141152113 [GRCh38]
Chr5:140531694 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1477G>T (p.Asp493Tyr) single nucleotide variant Inborn genetic diseases [RCV002789730] Chr5:141151734 [GRCh38]
Chr5:140531315 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.2194G>A (p.Gly732Arg) single nucleotide variant Inborn genetic diseases [RCV002826710] Chr5:141152451 [GRCh38]
Chr5:140532032 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.2026C>G (p.Pro676Ala) single nucleotide variant Inborn genetic diseases [RCV002713081] Chr5:141152283 [GRCh38]
Chr5:140531864 [GRCh37]
Chr5:5q31.3
likely benign
NM_018939.4(PCDHB6):c.110A>C (p.Glu37Ala) single nucleotide variant Inborn genetic diseases [RCV002957016] Chr5:141150367 [GRCh38]
Chr5:140529948 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.2312A>G (p.Asn771Ser) single nucleotide variant Inborn genetic diseases [RCV002803542] Chr5:141152569 [GRCh38]
Chr5:140532150 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1037C>T (p.Thr346Ile) single nucleotide variant Inborn genetic diseases [RCV002955318] Chr5:141151294 [GRCh38]
Chr5:140530875 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1100G>C (p.Ser367Thr) single nucleotide variant Inborn genetic diseases [RCV002939218] Chr5:141151357 [GRCh38]
Chr5:140530938 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.137A>G (p.Asn46Ser) single nucleotide variant Inborn genetic diseases [RCV002897773] Chr5:141150394 [GRCh38]
Chr5:140529975 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.796A>G (p.Arg266Gly) single nucleotide variant Inborn genetic diseases [RCV002672308] Chr5:141151053 [GRCh38]
Chr5:140530634 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1240G>C (p.Glu414Gln) single nucleotide variant Inborn genetic diseases [RCV002959469] Chr5:141151497 [GRCh38]
Chr5:140531078 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1850C>A (p.Ala617Glu) single nucleotide variant Inborn genetic diseases [RCV002652606] Chr5:141152107 [GRCh38]
Chr5:140531688 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.535G>T (p.Val179Phe) single nucleotide variant Inborn genetic diseases [RCV002656060] Chr5:141150792 [GRCh38]
Chr5:140530373 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1011C>A (p.Asp337Glu) single nucleotide variant Inborn genetic diseases [RCV002723669] Chr5:141151268 [GRCh38]
Chr5:140530849 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1562C>T (p.Ala521Val) single nucleotide variant Inborn genetic diseases [RCV002944739] Chr5:141151819 [GRCh38]
Chr5:140531400 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.298C>T (p.Pro100Ser) single nucleotide variant Inborn genetic diseases [RCV003218035] Chr5:141150555 [GRCh38]
Chr5:140530136 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1970A>G (p.His657Arg) single nucleotide variant Inborn genetic diseases [RCV003202087] Chr5:141152227 [GRCh38]
Chr5:140531808 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1423G>A (p.Asp475Asn) single nucleotide variant Inborn genetic diseases [RCV003208197] Chr5:141151680 [GRCh38]
Chr5:140531261 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.2081C>T (p.Ser694Leu) single nucleotide variant Inborn genetic diseases [RCV003210939] Chr5:141152338 [GRCh38]
Chr5:140531919 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.2027C>G (p.Pro676Arg) single nucleotide variant Inborn genetic diseases [RCV003287481] Chr5:141152284 [GRCh38]
Chr5:140531865 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.200T>A (p.Phe67Tyr) single nucleotide variant Inborn genetic diseases [RCV003264582] Chr5:141150457 [GRCh38]
Chr5:140530038 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1301G>A (p.Ser434Asn) single nucleotide variant Inborn genetic diseases [RCV003378705] Chr5:141151558 [GRCh38]
Chr5:140531139 [GRCh37]
Chr5:5q31.3
likely benign
NM_018939.4(PCDHB6):c.815C>G (p.Ser272Trp) single nucleotide variant Inborn genetic diseases [RCV003347590] Chr5:141151072 [GRCh38]
Chr5:140530653 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.2222G>A (p.Gly741Glu) single nucleotide variant Inborn genetic diseases [RCV003347607] Chr5:141152479 [GRCh38]
Chr5:140532060 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1887C>A (p.Ser629Arg) single nucleotide variant Inborn genetic diseases [RCV003384736] Chr5:141152144 [GRCh38]
Chr5:140531725 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_018939.4(PCDHB6):c.1639T>G (p.Leu547Val) single nucleotide variant not provided [RCV003428631] Chr5:141151896 [GRCh38]
Chr5:140531477 [GRCh37]
Chr5:5q31.3
likely benign
NM_018939.4(PCDHB6):c.1860C>G (p.Gly620=) single nucleotide variant not provided [RCV003428633] Chr5:141152117 [GRCh38]
Chr5:140531698 [GRCh37]
Chr5:5q31.3
likely benign
NM_018939.4(PCDHB6):c.1998G>A (p.Gln666=) single nucleotide variant not provided [RCV003429825] Chr5:141152255 [GRCh38]
Chr5:140531836 [GRCh37]
Chr5:5q31.3
likely benign
NM_018939.4(PCDHB6):c.1659C>T (p.Asn553=) single nucleotide variant not provided [RCV003428632] Chr5:141151916 [GRCh38]
Chr5:140531497 [GRCh37]
Chr5:5q31.3
likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:263
Count of miRNA genes:169
Interacting mature miRNAs:173
Transcripts:ENST00000231136, ENST00000543635
Prediction methods:Miranda, Rnahybrid
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
RH91958  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375140,532,601 - 140,532,783UniSTSGRCh37
Build 365140,512,785 - 140,512,967RGDNCBI36
Celera5136,609,415 - 136,609,597RGD
Cytogenetic Map5q31UniSTS
HuRef5135,677,299 - 135,677,481UniSTS
GeneMap99-GB4 RH Map5531.62UniSTS


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 adipose tissue appendage entire extraembryonic component
High
Medium 3 2 9 7 1 7 24 5 26 13 34 33
Low 1678 1692 1068 159 186 46 3165 1011 3510 243 1251 1386 117 1150 1934 2
Below cutoff 668 732 579 393 613 348 1126 1164 169 147 119 150 50 54 851 1

Sequence


RefSeq Acc Id: ENST00000231136   ⟹   ENSP00000231136
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5141,150,057 - 141,153,287 (+)Ensembl
RefSeq Acc Id: ENST00000622991   ⟹   ENSP00000485034
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5141,150,102 - 141,152,914 (+)Ensembl
RefSeq Acc Id: NM_001303145   ⟹   NP_001290074
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,150,057 - 141,153,287 (+)NCBI
CHM1_15139,962,794 - 139,966,059 (+)NCBI
T2T-CHM13v2.05141,675,376 - 141,678,606 (+)NCBI
Sequence:
RefSeq Acc Id: NM_018939   ⟹   NP_061762
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,150,057 - 141,153,287 (+)NCBI
GRCh375140,529,839 - 140,532,868 (+)RGD
Build 365140,510,023 - 140,513,052 (+)NCBI Archive
Celera5136,606,652 - 136,609,682 (+)RGD
HuRef5135,674,536 - 135,677,566 (+)ENTREZGENE
CHM1_15139,962,794 - 139,966,059 (+)NCBI
T2T-CHM13v2.05141,675,376 - 141,678,606 (+)NCBI
Sequence:
RefSeq Acc Id: NP_061762   ⟸   NM_018939
- Peptide Label: isoform 1 precursor
- UniProtKB: B2R8R9 (UniProtKB/Swiss-Prot),   Q9Y5E3 (UniProtKB/Swiss-Prot),   B4DSB6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001290074   ⟸   NM_001303145
- Peptide Label: isoform 2
- UniProtKB: A0A096LNH7 (UniProtKB/TrEMBL),   B4DSB6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000485034   ⟸   ENST00000622991
RefSeq Acc Id: ENSP00000231136   ⟸   ENST00000231136
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9Y5E3-F1-model_v2 AlphaFold Q9Y5E3 1-794 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:8691 AgrOrtholog
COSMIC PCDHB6 COSMIC
Ensembl Genes ENSG00000113211 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSG00000291679 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000231136 ENTREZGENE
  ENST00000231136.4 UniProtKB/Swiss-Prot
  ENST00000622991 ENTREZGENE
  ENST00000622991.1 UniProtKB/TrEMBL
  ENST00000708361.1 UniProtKB/Swiss-Prot
Gene3D-CATH Cadherins UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000113211 GTEx
  ENSG00000291679 GTEx
HGNC ID HGNC:8691 ENTREZGENE
Human Proteome Map PCDHB6 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
KEGG Report hsa:56130 UniProtKB/Swiss-Prot
NCBI Gene 56130 ENTREZGENE
OMIM 606332 OMIM
PANTHER CADHERIN-87A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTOCADHERIN BETA-6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/Swiss-Prot
  Cadherin_C_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA33040 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 SSF49313 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A096LNH7 ENTREZGENE, UniProtKB/TrEMBL
  B2R8R9 ENTREZGENE
  B4DSB6 ENTREZGENE, UniProtKB/TrEMBL
  PCDB6_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary B2R8R9 UniProtKB/Swiss-Prot