Incidental Mutation 'R2261:Pcdh1'
ID 243829
Institutional Source Beutler Lab
Gene Symbol Pcdh1
Ensembl Gene ENSMUSG00000051375
Gene Name protocadherin 1
Synonyms 2010005A06Rik
MMRRC Submission 040261-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.365) question?
Stock # R2261 (G1)
Quality Score 225
Status Validated
Chromosome 18
Chromosomal Location 38318967-38345023 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 38331710 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Histidine at position 431 (L431H)
Ref Sequence ENSEMBL: ENSMUSP00000125576 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000057185] [ENSMUST00000159405] [ENSMUST00000160721] [ENSMUST00000161701] [ENSMUST00000193828] [ENSMUST00000194312]
AlphaFold Q8CFX3
Predicted Effect probably benign
Transcript: ENSMUST00000057185
AA Change: L570H

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000055199
Gene: ENSMUSG00000051375
AA Change: L570H

DomainStartEndE-ValueType
signal peptide 1 33 N/A INTRINSIC
Pfam:Cadherin_2 36 120 2e-8 PFAM
CA 168 256 5.18e-18 SMART
CA 280 363 5.68e-24 SMART
CA 395 482 1.84e-23 SMART
CA 506 588 2.99e-32 SMART
CA 612 691 9.36e-25 SMART
CA 717 798 9.9e-15 SMART
transmembrane domain 830 852 N/A INTRINSIC
low complexity region 876 903 N/A INTRINSIC
low complexity region 951 964 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000159405
AA Change: L570H

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000125309
Gene: ENSMUSG00000051375
AA Change: L570H

DomainStartEndE-ValueType
signal peptide 1 33 N/A INTRINSIC
Pfam:Cadherin_2 36 120 2e-8 PFAM
CA 168 256 5.18e-18 SMART
CA 280 363 5.68e-24 SMART
CA 395 482 1.84e-23 SMART
CA 506 588 2.99e-32 SMART
CA 612 691 9.36e-25 SMART
CA 717 798 9.9e-15 SMART
transmembrane domain 830 852 N/A INTRINSIC
low complexity region 876 903 N/A INTRINSIC
low complexity region 951 964 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000160721
SMART Domains Protein: ENSMUSP00000124732
Gene: ENSMUSG00000051375

DomainStartEndE-ValueType
signal peptide 1 33 N/A INTRINSIC
Pfam:Cadherin_2 36 120 9.9e-10 PFAM
CA 168 256 5.18e-18 SMART
low complexity region 310 321 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000161701
AA Change: L431H

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: L431H

DomainStartEndE-ValueType
CA 29 117 5.18e-18 SMART
CA 141 224 5.68e-24 SMART
CA 256 343 1.84e-23 SMART
CA 367 449 2.99e-32 SMART
CA 473 552 9.36e-25 SMART
CA 578 659 9.9e-15 SMART
transmembrane domain 691 713 N/A INTRINSIC
low complexity region 737 764 N/A INTRINSIC
low complexity region 812 825 N/A INTRINSIC
low complexity region 903 914 N/A INTRINSIC
low complexity region 1029 1040 N/A INTRINSIC
low complexity region 1059 1071 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000193828
SMART Domains Protein: ENSMUSP00000142328
Gene: ENSMUSG00000051375

DomainStartEndE-ValueType
low complexity region 18 48 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000194312
Meta Mutation Damage Score 0.4217 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 97.2%
  • 20x: 94.7%
Validation Efficiency 98% (60/61)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 A T 11: 9,242,288 (GRCm39) M1384L probably benign Het
Ahdc1 A G 4: 132,790,474 (GRCm39) T572A unknown Het
Arhgap31 T A 16: 38,429,639 (GRCm39) Q412L probably damaging Het
Arsi T C 18: 61,049,737 (GRCm39) Y207H probably damaging Het
Bco1 T C 8: 117,859,764 (GRCm39) L489S probably damaging Het
Cacna1g T A 11: 94,347,961 (GRCm39) H709L probably benign Het
Cacna1h T C 17: 25,652,139 (GRCm39) T2A possibly damaging Het
Casz1 G T 4: 149,013,556 (GRCm39) R40L probably damaging Het
Cdh23 A G 10: 60,152,907 (GRCm39) V2372A probably damaging Het
Cdk17 T A 10: 93,047,820 (GRCm39) S56T possibly damaging Het
Ces2h T A 8: 105,743,191 (GRCm39) M142K probably damaging Het
Cfap69 C A 5: 5,646,018 (GRCm39) V561F probably damaging Het
Col1a2 G A 6: 4,518,822 (GRCm39) probably benign Het
Dnah11 T A 12: 117,843,760 (GRCm39) M4362L probably benign Het
Dnah11 T C 12: 117,930,374 (GRCm39) T3324A probably damaging Het
Dnajc3 A G 14: 119,198,232 (GRCm39) Q118R probably damaging Het
Dok4 A T 8: 95,593,140 (GRCm39) C182S probably damaging Het
Fam184a A G 10: 53,523,666 (GRCm39) probably null Het
Fanca A G 8: 124,016,098 (GRCm39) probably null Het
Flt3 G A 5: 147,284,873 (GRCm39) P748L probably benign Het
Gbp2b G A 3: 142,312,496 (GRCm39) S293N probably benign Het
Gbp8 T C 5: 105,163,999 (GRCm39) Q433R possibly damaging Het
Gm12874 G A 4: 122,487,533 (GRCm39) noncoding transcript Het
Golgb1 T A 16: 36,713,722 (GRCm39) F234L probably damaging Het
Gpr65 A T 12: 98,241,494 (GRCm39) N49I probably damaging Het
Grip1 G A 10: 119,821,489 (GRCm39) V385M probably benign Het
Ltbp3 G A 19: 5,804,050 (GRCm39) R854Q probably benign Het
Mast4 A G 13: 102,934,715 (GRCm39) probably benign Het
Mia3 A G 1: 183,115,647 (GRCm39) Y295H probably benign Het
Morc3 T A 16: 93,650,109 (GRCm39) probably benign Het
Muc6 G A 7: 141,218,313 (GRCm39) S2120F possibly damaging Het
Nell1 C T 7: 50,210,569 (GRCm39) T494I possibly damaging Het
Npy2r A G 3: 82,448,346 (GRCm39) V30A possibly damaging Het
Nsd2 A T 5: 34,042,871 (GRCm39) Q1045L probably damaging Het
Or51t4 T C 7: 102,598,464 (GRCm39) F254S probably damaging Het
Or5d40 T A 2: 88,015,965 (GRCm39) I248N probably damaging Het
Otub1 T A 19: 7,176,861 (GRCm39) probably null Het
Pdgfra T C 5: 75,346,184 (GRCm39) V778A probably benign Het
Plekhm2 C T 4: 141,370,043 (GRCm39) E29K probably damaging Het
Ralgapa2 T C 2: 146,184,603 (GRCm39) N1468S probably damaging Het
Rnf111 T C 9: 70,383,673 (GRCm39) S87G probably benign Het
Ryr3 C G 2: 112,506,218 (GRCm39) R3443P probably damaging Het
Saxo1 C T 4: 86,397,212 (GRCm39) D109N probably damaging Het
Slc19a3 A T 1: 83,000,678 (GRCm39) F113Y probably damaging Het
Slc20a1 A G 2: 129,048,394 (GRCm39) R260G possibly damaging Het
Slk T C 19: 47,625,791 (GRCm39) I1090T probably damaging Het
Spr-ps1 G T 6: 85,132,945 (GRCm39) noncoding transcript Het
Ssh1 T C 5: 114,080,764 (GRCm39) S867G possibly damaging Het
St18 T A 1: 6,915,796 (GRCm39) C814S probably damaging Het
Stmn2 T C 3: 8,606,955 (GRCm39) F25S probably damaging Het
Taar3 A G 10: 23,826,053 (GRCm39) I200V probably benign Het
Tmem184c T C 8: 78,323,804 (GRCm39) T353A probably damaging Het
Tmem184c A G 8: 78,323,672 (GRCm39) Y397H probably damaging Het
Tuba1c A G 15: 98,935,757 (GRCm39) H406R probably damaging Het
Ubr4 T C 4: 139,140,773 (GRCm39) S1231P probably damaging Het
Ubr5 A T 15: 37,988,528 (GRCm39) D2143E probably damaging Het
Vmn2r6 T C 3: 64,464,090 (GRCm39) N248S probably benign Het
Vmn2r63 G T 7: 42,578,031 (GRCm39) T169N probably benign Het
Zfp37 A T 4: 62,109,873 (GRCm39) L397Q probably damaging Het
Zmym2 G A 14: 57,165,719 (GRCm39) E681K probably damaging Het
Other mutations in Pcdh1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00714:Pcdh1 APN 18 38,331,782 (GRCm39) missense possibly damaging 0.65
IGL00919:Pcdh1 APN 18 38,335,865 (GRCm39) nonsense probably null
IGL01744:Pcdh1 APN 18 38,336,302 (GRCm39) missense probably damaging 1.00
PIT4260001:Pcdh1 UTSW 18 38,336,419 (GRCm39) missense probably damaging 0.99
R0542:Pcdh1 UTSW 18 38,322,975 (GRCm39) missense probably damaging 0.99
R1449:Pcdh1 UTSW 18 38,322,929 (GRCm39) missense probably damaging 0.99
R1540:Pcdh1 UTSW 18 38,322,779 (GRCm39) missense probably benign 0.01
R1642:Pcdh1 UTSW 18 38,332,283 (GRCm39) missense possibly damaging 0.84
R1672:Pcdh1 UTSW 18 38,325,233 (GRCm39) missense probably damaging 1.00
R1695:Pcdh1 UTSW 18 38,335,921 (GRCm39) missense probably damaging 1.00
R1727:Pcdh1 UTSW 18 38,336,085 (GRCm39) nonsense probably null
R1781:Pcdh1 UTSW 18 38,322,977 (GRCm39) missense probably damaging 1.00
R1793:Pcdh1 UTSW 18 38,331,938 (GRCm39) missense probably damaging 0.99
R1839:Pcdh1 UTSW 18 38,332,538 (GRCm39) missense possibly damaging 0.82
R1843:Pcdh1 UTSW 18 38,325,278 (GRCm39) splice site probably null
R1882:Pcdh1 UTSW 18 38,335,895 (GRCm39) missense possibly damaging 0.49
R2262:Pcdh1 UTSW 18 38,331,710 (GRCm39) missense probably benign 0.01
R2263:Pcdh1 UTSW 18 38,331,710 (GRCm39) missense probably benign 0.01
R2511:Pcdh1 UTSW 18 38,332,532 (GRCm39) missense possibly damaging 0.95
R2937:Pcdh1 UTSW 18 38,322,815 (GRCm39) missense probably benign 0.40
R3941:Pcdh1 UTSW 18 38,332,511 (GRCm39) missense probably benign 0.02
R3942:Pcdh1 UTSW 18 38,332,511 (GRCm39) missense probably benign 0.02
R4057:Pcdh1 UTSW 18 38,331,950 (GRCm39) missense probably damaging 0.98
R4155:Pcdh1 UTSW 18 38,336,159 (GRCm39) missense probably damaging 0.99
R4169:Pcdh1 UTSW 18 38,331,358 (GRCm39) missense probably damaging 1.00
R4617:Pcdh1 UTSW 18 38,330,913 (GRCm39) missense probably benign 0.00
R4690:Pcdh1 UTSW 18 38,336,528 (GRCm39) missense probably benign 0.33
R4825:Pcdh1 UTSW 18 38,322,912 (GRCm39) missense possibly damaging 0.77
R5201:Pcdh1 UTSW 18 38,331,971 (GRCm39) missense probably damaging 0.98
R5266:Pcdh1 UTSW 18 38,325,252 (GRCm39) missense probably damaging 1.00
R5267:Pcdh1 UTSW 18 38,325,252 (GRCm39) missense probably damaging 1.00
R5351:Pcdh1 UTSW 18 38,330,819 (GRCm39) missense probably damaging 1.00
R5568:Pcdh1 UTSW 18 38,330,420 (GRCm39) missense probably damaging 1.00
R5729:Pcdh1 UTSW 18 38,335,999 (GRCm39) missense probably damaging 1.00
R5731:Pcdh1 UTSW 18 38,331,651 (GRCm39) missense probably damaging 1.00
R6043:Pcdh1 UTSW 18 38,336,327 (GRCm39) missense probably damaging 0.97
R6278:Pcdh1 UTSW 18 38,332,263 (GRCm39) missense probably benign 0.29
R6333:Pcdh1 UTSW 18 38,331,860 (GRCm39) missense probably benign 0.25
R6498:Pcdh1 UTSW 18 38,330,490 (GRCm39) missense probably benign 0.18
R6937:Pcdh1 UTSW 18 38,336,528 (GRCm39) missense possibly damaging 0.86
R6994:Pcdh1 UTSW 18 38,331,553 (GRCm39) missense probably damaging 1.00
R7242:Pcdh1 UTSW 18 38,336,270 (GRCm39) missense probably benign 0.06
R7289:Pcdh1 UTSW 18 38,322,966 (GRCm39) missense probably damaging 0.99
R7391:Pcdh1 UTSW 18 38,335,838 (GRCm39) missense possibly damaging 0.95
R7702:Pcdh1 UTSW 18 38,336,569 (GRCm39) missense unknown
R7738:Pcdh1 UTSW 18 38,330,529 (GRCm39) missense probably benign 0.02
R7849:Pcdh1 UTSW 18 38,322,662 (GRCm39) missense probably benign 0.01
R7941:Pcdh1 UTSW 18 38,332,133 (GRCm39) missense probably damaging 1.00
R8109:Pcdh1 UTSW 18 38,332,049 (GRCm39) missense probably damaging 1.00
R8675:Pcdh1 UTSW 18 38,332,229 (GRCm39) missense probably damaging 1.00
R8851:Pcdh1 UTSW 18 38,325,155 (GRCm39) missense probably damaging 1.00
R8947:Pcdh1 UTSW 18 38,332,073 (GRCm39) missense possibly damaging 0.89
R9443:Pcdh1 UTSW 18 38,330,633 (GRCm39) missense probably damaging 1.00
R9448:Pcdh1 UTSW 18 38,330,492 (GRCm39) missense probably damaging 1.00
R9608:Pcdh1 UTSW 18 38,330,904 (GRCm39) missense possibly damaging 0.91
X0027:Pcdh1 UTSW 18 38,322,841 (GRCm39) nonsense probably null
Z1088:Pcdh1 UTSW 18 38,331,120 (GRCm39) missense probably damaging 1.00
Z1176:Pcdh1 UTSW 18 38,331,741 (GRCm39) missense possibly damaging 0.79
Predicted Primers PCR Primer
(F):5'- ATGGTGCCTGTGCCATTCTG -3'
(R):5'- TGACTCTGGCTCTAACGCAG -3'

Sequencing Primer
(F):5'- GCCTGTGCCATTCTGGATAACAAAG -3'
(R):5'- TAACGCAGAGCTAGTATACTCGCTG -3'
Posted On 2014-10-16