PCDHB16 (protocadherin beta 16) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: PCDHB16 (protocadherin beta 16) Homo sapiens
Analyze
Symbol: PCDHB16
Name: protocadherin beta 16
RGD ID: 1343753
HGNC Page HGNC:14546
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in cell adhesion. Predicted to be located in plasma membrane and synapse.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: cadherin ME1; KIAA1621; ME1; PCDH-beta-16; PCDH-BETA16; PCDH3X; PCDHB8a; PCDHbeta 16; protocadherin beta 8a; protocadherin beta-16; protocadherin-3x
RGD Orthologs
Mouse
Rat
Pig
Green Monkey
Alliance Genes
More Info more info ...
Related Pseudogenes: PCDHB18P  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385141,182,387 - 141,186,226 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5141,182,387 - 141,186,226 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,561,962 - 140,565,801 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,541,164 - 140,545,980 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,541,163 - 140,545,979NCBI
Celera5136,637,807 - 136,642,623 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,706,024 - 135,710,848 (+)NCBIHuRef
CHM1_15139,994,171 - 139,998,993 (+)NCBICHM1_1
T2T-CHM13v2.05141,707,702 - 141,711,541 (+)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)
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:9182820   PMID:10380929   PMID:10716726   PMID:10817752   PMID:10835267   PMID:10997877   PMID:11230163   PMID:11322959   PMID:12231349   PMID:12477932   PMID:12665801   PMID:14702039  
PMID:15489334   PMID:21873635   PMID:28514442   PMID:28611215   PMID:33961781  


Genomics

Comparative Map Data
PCDHB16
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385141,182,387 - 141,186,226 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5141,182,387 - 141,186,226 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,561,962 - 140,565,801 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,541,164 - 140,545,980 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,541,163 - 140,545,979NCBI
Celera5136,637,807 - 136,642,623 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,706,024 - 135,710,848 (+)NCBIHuRef
CHM1_15139,994,171 - 139,998,993 (+)NCBICHM1_1
T2T-CHM13v2.05141,707,702 - 141,711,541 (+)NCBIT2T-CHM13v2.0
Pcdhb17
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,618,040 - 37,621,345 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,617,848 - 37,622,507 (+)EnsemblGRCm39 Ensembl
GRCm381837,485,021 - 37,488,290 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,484,795 - 37,489,454 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,644,675 - 37,647,944 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,610,993 - 37,614,264 (+)NCBIMGSCv36mm8
Celera1838,836,325 - 38,839,594 (+)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.5NCBI
Pcdhb16
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81829,466,270 - 29,469,679 (+)NCBIGRCr8
mRatBN7.21829,192,260 - 29,195,669 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1829,192,124 - 29,200,539 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1829,319,386 - 29,322,795 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01830,081,387 - 30,084,796 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01829,416,697 - 29,420,106 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01830,560,799 - 30,565,316 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1830,562,178 - 30,564,577 (+)EnsemblRnor6.0rn6Rnor6.0
Celera1828,886,949 - 28,891,466 (+)NCBICelera
Cytogenetic Map18p11NCBI
LOC100739498
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.12142,873,080 - 142,877,989 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22149,032,347 - 149,035,962 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PCDHB16
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12343,806,794 - 43,811,412 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603434,039,496 - 34,043,878 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in PCDHB16
44 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 5q31.3(chr5:141185055-141211630)x1 copy number loss See cases [RCV000052580] Chr5:141185055..141211630 [GRCh38]
Chr5:140564630..140591202 [GRCh37]
Chr5:140544814..140571386 [NCBI36]
Chr5:5q31.3
uncertain significance
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_020957.3(PCDHB16):c.2014C>T (p.Pro672Ser) single nucleotide variant Malignant melanoma [RCV000066718] Chr5:141184573 [GRCh38]
Chr5:140564148 [GRCh37]
Chr5:140544332 [NCBI36]
Chr5:5q31.3
not provided
NM_020957.3(PCDHB16):c.2015C>T (p.Pro672Leu) single nucleotide variant Malignant melanoma [RCV000066719] Chr5:141184574 [GRCh38]
Chr5:140564149 [GRCh37]
Chr5:140544333 [NCBI36]
Chr5:5q31.3
not provided
NM_019119.4(PCDHB9):c.1219G>A (p.Gly407Ser) single nucleotide variant Malignant melanoma [RCV000061151] Chr5:141188537 [GRCh38]
Chr5:140568110 [GRCh37]
Chr5:140548294 [NCBI36]
Chr5:5q31.3
not provided
NM_019120.4(PCDHB8):c.538C>T (p.Arg180Trp) single nucleotide variant Malignant melanoma [RCV000066714] Chr5:141178572 [GRCh38]
Chr5:140558153 [GRCh37]
Chr5:140538337 [NCBI36]
Chr5:5q31.3
not provided
NM_019120.4(PCDHB8):c.931G>A (p.Glu311Lys) single nucleotide variant Malignant melanoma [RCV000066715] Chr5:141178965 [GRCh38]
Chr5:140558546 [GRCh37]
Chr5:140538730 [NCBI36]
Chr5:5q31.3
not provided
NM_019120.4(PCDHB8):c.1848C>T (p.Phe616=) single nucleotide variant Malignant melanoma [RCV000066716] Chr5:141179882 [GRCh38]
Chr5:140559463 [GRCh37]
Chr5:140539647 [NCBI36]
Chr5:5q31.3
not provided
NM_019120.4(PCDHB8):c.2127C>T (p.Phe709=) single nucleotide variant Malignant melanoma [RCV000066717] Chr5:141180161 [GRCh38]
Chr5:140559742 [GRCh37]
Chr5:140539926 [NCBI36]
Chr5:5q31.3
not provided
NM_019119.4(PCDHB9):c.1845C>T (p.Phe615=) single nucleotide variant Malignant melanoma [RCV000066720] Chr5:141189163 [GRCh38]
Chr5:140568736 [GRCh37]
Chr5:140548920 [NCBI36]
Chr5:5q31.3
not provided
NM_019120.4(PCDHB8):c.385G>A (p.Asp129Asn) single nucleotide variant Malignant melanoma [RCV000061149] Chr5:141178419 [GRCh38]
Chr5:140558000 [GRCh37]
Chr5:140538184 [NCBI36]
Chr5:5q31.3
not provided
NM_019120.4(PCDHB8):c.713A>G (p.Asp238Gly) single nucleotide variant Malignant melanoma [RCV000061150] Chr5:141178747 [GRCh38]
Chr5:140558328 [GRCh37]
Chr5:140538512 [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
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 5q31.3(chr5:140559899-140580412)x1 copy number loss See cases [RCV000449410] Chr5:140559899..140580412 [GRCh37]
Chr5:5q31.3
likely benign
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_020957.4(PCDHB16):c.597G>C (p.Glu199Asp) single nucleotide variant Inborn genetic diseases [RCV003279746] Chr5:141183156 [GRCh38]
Chr5:140562731 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1849G>T (p.Val617Leu) single nucleotide variant Inborn genetic diseases [RCV003295096] Chr5:141184408 [GRCh38]
Chr5:140563983 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1431C>G (p.Asp477Glu) single nucleotide variant Inborn genetic diseases [RCV003299259] Chr5:141183990 [GRCh38]
Chr5:140563565 [GRCh37]
Chr5:5q31.3
uncertain significance
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
NM_020957.4(PCDHB16):c.1086G>T (p.Glu362Asp) single nucleotide variant Inborn genetic diseases [RCV003299899] Chr5:141183645 [GRCh38]
Chr5:140563220 [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
GRCh37/hg19 5q31.3(chr5:140558308-140594381)x1 copy number loss not provided [RCV000745227] Chr5:140558308..140594381 [GRCh37]
Chr5:5q31.3
benign
GRCh37/hg19 5q31.3(chr5:140559849-140606802)x3 copy number gain not provided [RCV000745228] Chr5:140559849..140606802 [GRCh37]
Chr5:5q31.3
benign
Single allele deletion Neurodevelopmental disorder [RCV000787436] Chr5:14685137..149511942 [GRCh37]
Chr5:5p15.2-q32
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
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_020957.4(PCDHB16):c.1277T>C (p.Met426Thr) single nucleotide variant Inborn genetic diseases [RCV003295408] Chr5:141183836 [GRCh38]
Chr5:140563411 [GRCh37]
Chr5:5q31.3
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
GRCh37/hg19 5q31.3(chr5:140082762-140773954)x3 copy number gain not provided [RCV002474614] Chr5:140082762..140773954 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.901G>C (p.Val301Leu) single nucleotide variant Inborn genetic diseases [RCV002992870] Chr5:141183460 [GRCh38]
Chr5:140563035 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1384G>C (p.Glu462Gln) single nucleotide variant Inborn genetic diseases [RCV002841854] Chr5:141183943 [GRCh38]
Chr5:140563518 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.2194T>C (p.Phe732Leu) single nucleotide variant Inborn genetic diseases [RCV002997657] Chr5:141184753 [GRCh38]
Chr5:140564328 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.2174G>A (p.Cys725Tyr) single nucleotide variant Inborn genetic diseases [RCV002902090] Chr5:141184733 [GRCh38]
Chr5:140564308 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1615C>T (p.Pro539Ser) single nucleotide variant Inborn genetic diseases [RCV002793896] Chr5:141184174 [GRCh38]
Chr5:140563749 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1993G>A (p.Gly665Ser) single nucleotide variant Inborn genetic diseases [RCV002688199] Chr5:141184552 [GRCh38]
Chr5:140564127 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1171T>G (p.Phe391Val) single nucleotide variant Inborn genetic diseases [RCV002732678] Chr5:141183730 [GRCh38]
Chr5:140563305 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1955G>T (p.Arg652Leu) single nucleotide variant Inborn genetic diseases [RCV002752022] Chr5:141184514 [GRCh38]
Chr5:140564089 [GRCh37]
Chr5:5q31.3
likely benign
NM_020957.4(PCDHB16):c.428C>A (p.Pro143Gln) single nucleotide variant Inborn genetic diseases [RCV002793442] Chr5:141182987 [GRCh38]
Chr5:140562562 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1516A>G (p.Ile506Val) single nucleotide variant Inborn genetic diseases [RCV002836474] Chr5:141184075 [GRCh38]
Chr5:140563650 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1607G>C (p.Arg536Pro) single nucleotide variant Inborn genetic diseases [RCV002990381] Chr5:141184166 [GRCh38]
Chr5:140563741 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1610G>C (p.Gly537Ala) single nucleotide variant Inborn genetic diseases [RCV002793895] Chr5:141184169 [GRCh38]
Chr5:140563744 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1399G>A (p.Ala467Thr) single nucleotide variant Inborn genetic diseases [RCV002784874] Chr5:141183958 [GRCh38]
Chr5:140563533 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.754C>G (p.Pro252Ala) single nucleotide variant Inborn genetic diseases [RCV002823489] Chr5:141183313 [GRCh38]
Chr5:140562888 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.512A>C (p.Lys171Thr) single nucleotide variant Inborn genetic diseases [RCV002691790] Chr5:141183071 [GRCh38]
Chr5:140562646 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.322G>T (p.Val108Leu) single nucleotide variant Inborn genetic diseases [RCV002950506] Chr5:141182881 [GRCh38]
Chr5:140562456 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1584G>C (p.Glu528Asp) single nucleotide variant Inborn genetic diseases [RCV002693955] Chr5:141184143 [GRCh38]
Chr5:140563718 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.13T>A (p.Trp5Arg) single nucleotide variant Inborn genetic diseases [RCV002787975] Chr5:141182572 [GRCh38]
Chr5:140562147 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1214C>A (p.Thr405Lys) single nucleotide variant Inborn genetic diseases [RCV002641469] Chr5:141183773 [GRCh38]
Chr5:140563348 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.213C>G (p.Asn71Lys) single nucleotide variant Inborn genetic diseases [RCV002641168] Chr5:141182772 [GRCh38]
Chr5:140562347 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.821A>G (p.Asn274Ser) single nucleotide variant Inborn genetic diseases [RCV002826801] Chr5:141183380 [GRCh38]
Chr5:140562955 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.779T>A (p.Leu260Gln) single nucleotide variant Inborn genetic diseases [RCV002827860] Chr5:141183338 [GRCh38]
Chr5:140562913 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.284T>C (p.Leu95Pro) single nucleotide variant Inborn genetic diseases [RCV002984156] Chr5:141182843 [GRCh38]
Chr5:140562418 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1528A>T (p.Asn510Tyr) single nucleotide variant Inborn genetic diseases [RCV002954914] Chr5:141184087 [GRCh38]
Chr5:140563662 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.169A>T (p.Thr57Ser) single nucleotide variant Inborn genetic diseases [RCV002939562] Chr5:141182728 [GRCh38]
Chr5:140562303 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1146T>G (p.Ile382Met) single nucleotide variant Inborn genetic diseases [RCV002670585] Chr5:141183705 [GRCh38]
Chr5:140563280 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.184C>G (p.Arg62Gly) single nucleotide variant Inborn genetic diseases [RCV002878816] Chr5:141182743 [GRCh38]
Chr5:140562318 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1088T>C (p.Ile363Thr) single nucleotide variant Inborn genetic diseases [RCV002897697] Chr5:141183647 [GRCh38]
Chr5:140563222 [GRCh37]
Chr5:5q31.3
likely benign
NM_020957.4(PCDHB16):c.719C>T (p.Pro240Leu) single nucleotide variant Inborn genetic diseases [RCV002898327] Chr5:141183278 [GRCh38]
Chr5:140562853 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.2050A>C (p.Asn684His) single nucleotide variant Inborn genetic diseases [RCV002769333] Chr5:141184609 [GRCh38]
Chr5:140564184 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.338C>T (p.Pro113Leu) single nucleotide variant Inborn genetic diseases [RCV002835825] Chr5:141182897 [GRCh38]
Chr5:140562472 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.65G>A (p.Ser22Asn) single nucleotide variant Inborn genetic diseases [RCV002944522] Chr5:141182624 [GRCh38]
Chr5:140562199 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1062C>A (p.Ser354Arg) single nucleotide variant Inborn genetic diseases [RCV003255422] Chr5:141183621 [GRCh38]
Chr5:140563196 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1483G>A (p.Asp495Asn) single nucleotide variant Inborn genetic diseases [RCV003192317] Chr5:141184042 [GRCh38]
Chr5:140563617 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1894G>A (p.Glu632Lys) single nucleotide variant Inborn genetic diseases [RCV003197748] Chr5:141184453 [GRCh38]
Chr5:140564028 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.938C>G (p.Thr313Arg) single nucleotide variant Inborn genetic diseases [RCV003191830] Chr5:141183497 [GRCh38]
Chr5:140563072 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.23A>G (p.Asn8Ser) single nucleotide variant Inborn genetic diseases [RCV003264878] Chr5:141182582 [GRCh38]
Chr5:140562157 [GRCh37]
Chr5:5q31.3
likely benign
NM_020957.4(PCDHB16):c.1831G>A (p.Glu611Lys) single nucleotide variant Inborn genetic diseases [RCV003340403] Chr5:141184390 [GRCh38]
Chr5:140563965 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.2179A>G (p.Met727Val) single nucleotide variant Inborn genetic diseases [RCV003359467] Chr5:141184738 [GRCh38]
Chr5:140564313 [GRCh37]
Chr5:5q31.3
likely benign
NM_020957.4(PCDHB16):c.1907C>T (p.Ala636Val) single nucleotide variant Inborn genetic diseases [RCV003346062] Chr5:141184466 [GRCh38]
Chr5:140564041 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.1585T>A (p.Phe529Ile) single nucleotide variant Inborn genetic diseases [RCV003372313] Chr5:141184144 [GRCh38]
Chr5:140563719 [GRCh37]
Chr5:5q31.3
uncertain significance
NM_020957.4(PCDHB16):c.641C>T (p.Ala214Val) single nucleotide variant not provided [RCV003429831] Chr5:141183200 [GRCh38]
Chr5:140562775 [GRCh37]
Chr5:5q31.3
likely benign
NM_020957.4(PCDHB16):c.1647G>A (p.Val549=) single nucleotide variant not provided [RCV003429833] Chr5:141184206 [GRCh38]
Chr5:140563781 [GRCh37]
Chr5:5q31.3
likely benign
NM_020957.4(PCDHB16):c.1542C>T (p.Phe514=) single nucleotide variant not provided [RCV003429832] Chr5:141184101 [GRCh38]
Chr5:140563676 [GRCh37]
Chr5:5q31.3
likely benign
NM_020957.4(PCDHB16):c.1251T>C (p.Tyr417=) single nucleotide variant not provided [RCV003428636] Chr5:141183810 [GRCh38]
Chr5:140563385 [GRCh37]
Chr5:5q31.3
likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:499
Count of miRNA genes:388
Interacting mature miRNAs:396
Transcripts:ENST00000361016
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
RH92429  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375140,561,525 - 140,561,750UniSTSGRCh37
Build 365140,541,709 - 140,541,934RGDNCBI36
Celera5136,638,352 - 136,638,577RGD
Cytogenetic Map5q31UniSTS
HuRef5135,706,577 - 135,706,802UniSTS
GeneMap99-GB4 RH Map5531.62UniSTS
PCDHB16_1917  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375140,565,111 - 140,565,885UniSTSGRCh37
Build 365140,545,295 - 140,546,069RGDNCBI36
Celera5136,641,938 - 136,642,712RGD
HuRef5135,710,163 - 135,710,937UniSTS
D15S1390  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map19q13.33UniSTS
Cytogenetic Map10q26.3UniSTS
Cytogenetic Map7q34UniSTS
Cytogenetic Map17q21.33UniSTS
Cytogenetic Map18q11.2UniSTS
Cytogenetic Map16p11.2UniSTS
Cytogenetic Map8p11.22UniSTS
Cytogenetic Map10q23.2UniSTS
Cytogenetic Map15q21UniSTS
Cytogenetic Map6p25UniSTS
Cytogenetic Map1q21.3UniSTS
Cytogenetic Map8q24.22UniSTS
Cytogenetic Map6p23UniSTS
Cytogenetic Map12q13.3UniSTS
Cytogenetic Map1q32.1UniSTS
Cytogenetic Map5q31UniSTS
Cytogenetic Map16q24.1UniSTS
Cytogenetic Map20p13UniSTS
Cytogenetic Map7q22UniSTS
Cytogenetic Map1p34.2UniSTS
Cytogenetic Map11q23.3UniSTS
Cytogenetic Map12q22UniSTS
Cytogenetic Map18q12.1UniSTS
Cytogenetic Map19p13.11UniSTS
Cytogenetic Map10q24.32UniSTS
Cytogenetic Map4q26UniSTS
Cytogenetic Map6p21.1UniSTS
Cytogenetic Map11q12-q13UniSTS
Cytogenetic Map14q32.3UniSTS
Cytogenetic Map1p36.11UniSTS
Cytogenetic Map7q32.1UniSTS
Cytogenetic Map19p13.1UniSTS
Cytogenetic Map7p13-p12UniSTS
Cytogenetic Map10q25.2UniSTS
Cytogenetic Map3p14.1UniSTS
Cytogenetic Map8q22.1UniSTS
Cytogenetic Map4q21.1UniSTS
Cytogenetic Map12q13.12UniSTS
Cytogenetic Map1q21.2UniSTS
Cytogenetic Map19q13UniSTS
Cytogenetic Map7q21.3UniSTS
Cytogenetic Map17q21UniSTS
Cytogenetic Map18q21.3UniSTS
Cytogenetic Map22q13.33UniSTS
Cytogenetic Map1q25.2UniSTS
Cytogenetic Map12q13UniSTS
Cytogenetic Map1p32UniSTS
Cytogenetic Map15q23UniSTS
Cytogenetic Map14q21.3UniSTS
Cytogenetic Map8p23.1UniSTS
Cytogenetic Map10q24.2UniSTS
Cytogenetic Map7p13UniSTS


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 3 106 6 2 1 2 38 14 45 5 28 36 1 17
Low 1872 2058 1161 183 303 24 3720 1602 3352 146 1171 1363 165 1204 2254 3
Below cutoff 458 368 313 246 534 247 557 573 267 27 53 55 2 517 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_000017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_020957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB046841 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC074130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC244517 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF217757 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF282973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI684744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI926355 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK056460 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY013878 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC036062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CA438727 (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
  D88794 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HF584163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENST00000609684   ⟹   ENSP00000477314
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5141,182,387 - 141,186,226 (+)Ensembl
RefSeq Acc Id: ENST00000625044   ⟹   ENSP00000485449
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5141,182,403 - 141,184,269 (+)Ensembl
RefSeq Acc Id: NM_020957   ⟹   NP_066008
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385141,182,387 - 141,186,226 (+)NCBI
GRCh375140,560,980 - 140,566,710 (+)NCBI
Build 365140,541,164 - 140,545,980 (+)NCBI Archive
Celera5136,637,807 - 136,642,623 (+)RGD
HuRef5135,706,317 - 135,710,848 (+)NCBI
CHM1_15139,994,462 - 139,998,993 (+)NCBI
T2T-CHM13v2.05141,707,702 - 141,711,541 (+)NCBI
Sequence:
RefSeq Acc Id: NP_066008   ⟸   NM_020957
- Peptide Label: precursor
- UniProtKB: Q96SE9 (UniProtKB/Swiss-Prot),   Q8IYD5 (UniProtKB/Swiss-Prot),   B3KPK5 (UniProtKB/Swiss-Prot),   Q9HCF1 (UniProtKB/Swiss-Prot),   Q9NRJ7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000477314   ⟸   ENST00000609684
RefSeq Acc Id: ENSP00000485449   ⟸   ENST00000625044
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9NRJ7-F1-model_v2 AlphaFold Q9NRJ7 1-776 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:14546 AgrOrtholog
COSMIC PCDHB16 COSMIC
Ensembl Genes ENSG00000272674 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSG00000291684 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000609684 ENTREZGENE
  ENST00000609684.3 UniProtKB/Swiss-Prot
  ENST00000625044.1 UniProtKB/TrEMBL
  ENST00000708367.1 UniProtKB/Swiss-Prot
Gene3D-CATH Cadherins UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000272674 GTEx
  ENSG00000291684 GTEx
HGNC ID HGNC:14546 ENTREZGENE
Human Proteome Map PCDHB16 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
  Cadherin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_N UniProtKB/Swiss-Prot
KEGG Report hsa:57717 UniProtKB/Swiss-Prot
NCBI Gene 57717 ENTREZGENE
OMIM 606345 OMIM
PANTHER CADHERIN-87A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTOCADHERIN BETA-16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/Swiss-Prot
  Cadherin_C_2 UniProtKB/Swiss-Prot
PharmGKB PA33032 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 A0A096LP81_HUMAN UniProtKB/TrEMBL
  B3KPK5 ENTREZGENE
  L8E8M9_HUMAN UniProtKB/TrEMBL
  PCDBG_HUMAN UniProtKB/Swiss-Prot
  Q8IYD5 ENTREZGENE
  Q96SE9 ENTREZGENE
  Q9HCF1 ENTREZGENE
  Q9NRJ7 ENTREZGENE
UniProt Secondary B3KPK5 UniProtKB/Swiss-Prot
  Q8IYD5 UniProtKB/Swiss-Prot
  Q96SE9 UniProtKB/Swiss-Prot
  Q9HCF1 UniProtKB/Swiss-Prot