Incidental Mutation 'R5201:Pcdh1'
ID 400836
Institutional Source Beutler Lab
Gene Symbol Pcdh1
Ensembl Gene ENSMUSG00000051375
Gene Name protocadherin 1
Synonyms 2010005A06Rik
MMRRC Submission 042776-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.365) question?
Stock # R5201 (G1)
Quality Score 225
Status Not validated
Chromosome 18
Chromosomal Location 38318967-38345023 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 38331971 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Aspartic acid at position 344 (V344D)
Ref Sequence ENSEMBL: ENSMUSP00000125576 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000057185] [ENSMUST00000159405] [ENSMUST00000160721] [ENSMUST00000161701] [ENSMUST00000193828] [ENSMUST00000194312]
AlphaFold Q8CFX3
Predicted Effect probably damaging
Transcript: ENSMUST00000057185
AA Change: V483D

PolyPhen 2 Score 0.958 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000055199
Gene: ENSMUSG00000051375
AA Change: V483D

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 damaging
Transcript: ENSMUST00000159405
AA Change: V483D

PolyPhen 2 Score 0.958 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000125309
Gene: ENSMUSG00000051375
AA Change: V483D

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 damaging
Transcript: ENSMUST00000161701
AA Change: V344D

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: V344D

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
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 94.0%
Validation Efficiency
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: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930407I10Rik C A 15: 81,946,745 (GRCm39) T214N probably benign Het
Actn4 A T 7: 28,615,680 (GRCm39) probably null Het
Arap2 T C 5: 62,840,832 (GRCm39) E678G probably damaging Het
Atl2 T C 17: 80,172,580 (GRCm39) N130S probably benign Het
Cby2 A G 14: 75,821,449 (GRCm39) V101A probably damaging Het
Cyp2b10 A G 7: 25,616,419 (GRCm39) D342G probably damaging Het
Dnah6 A G 6: 73,172,715 (GRCm39) Y248H possibly damaging Het
Drd5 A T 5: 38,477,366 (GRCm39) M120L probably damaging Het
Duox1 A G 2: 122,158,403 (GRCm39) R629G probably benign Het
Dyrk1b A G 7: 27,884,521 (GRCm39) Y279C probably damaging Het
Efemp1 A T 11: 28,864,590 (GRCm39) I215L probably benign Het
Enpp6 C A 8: 47,518,486 (GRCm39) Q205K probably damaging Het
Fam170a A T 18: 50,415,193 (GRCm39) T280S probably benign Het
Fam222a G A 5: 114,749,127 (GRCm39) A108T possibly damaging Het
Fgd3 G T 13: 49,449,854 (GRCm39) P132T probably benign Het
Fzr1 A T 10: 81,203,362 (GRCm39) L399H probably damaging Het
Galnt15 G A 14: 31,771,822 (GRCm39) R289Q probably damaging Het
Hira T C 16: 18,770,865 (GRCm39) V834A probably damaging Het
Ilf3 T C 9: 21,300,679 (GRCm39) L93P probably damaging Het
Itgae G A 11: 73,001,382 (GRCm39) R71Q probably benign Het
Itprid1 T C 6: 55,944,991 (GRCm39) S571P probably benign Het
Kif14 T A 1: 136,431,145 (GRCm39) S1181T probably benign Het
Lrig3 C A 10: 125,849,020 (GRCm39) P946Q possibly damaging Het
Macf1 A T 4: 123,369,738 (GRCm39) C1674* probably null Het
Malt1 A G 18: 65,609,126 (GRCm39) K710R probably benign Het
Man1a2 A T 3: 100,524,328 (GRCm39) N373K probably benign Het
Mpped2 A G 2: 106,529,847 (GRCm39) N32S possibly damaging Het
Mrtfb A C 16: 13,219,456 (GRCm39) T701P probably benign Het
Myh10 A T 11: 68,674,021 (GRCm39) T652S probably damaging Het
Nfia A G 4: 97,999,462 (GRCm39) Y485C probably damaging Het
Olfml2b A T 1: 170,496,433 (GRCm39) T355S probably benign Het
Or10q3 A T 19: 11,847,995 (GRCm39) I195K probably benign Het
Otx1 C A 11: 21,947,037 (GRCm39) A91S probably damaging Het
Plekhn1 C A 4: 156,314,984 (GRCm39) V558L probably benign Het
Prr14l A G 5: 32,987,591 (GRCm39) S635P possibly damaging Het
Prss46 T A 9: 110,680,543 (GRCm39) C229* probably null Het
Rad50 A G 11: 53,589,647 (GRCm39) probably null Het
Slc27a3 A T 3: 90,296,526 (GRCm39) L191Q probably benign Het
Surf4 A G 2: 26,823,778 (GRCm39) probably benign Het
Taf3 A G 2: 9,956,995 (GRCm39) S391P probably damaging Het
Tep1 A C 14: 51,105,567 (GRCm39) L151R probably benign Het
Tmprss11d A C 5: 86,457,214 (GRCm39) N148K possibly damaging Het
Tpd52l2 G A 2: 181,156,879 (GRCm39) V172I probably benign Het
Vmn2r77 A G 7: 86,460,846 (GRCm39) D724G probably damaging Het
Wdr75 T A 1: 45,862,519 (GRCm39) D779E probably benign Het
Zfp943 A T 17: 22,211,794 (GRCm39) K293N 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
R2261:Pcdh1 UTSW 18 38,331,710 (GRCm39) missense probably benign 0.01
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
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'- ATCTCTCCATTCTCGGGTGAG -3'
(R):5'- AACATATCAGAGGACGTGGC -3'

Sequencing Primer
(F):5'- GATAGTGAAGAGCCCTTGGGC -3'
(R):5'- TCACCTGTGTCGTAGCAGG -3'
Posted On 2016-07-06