Incidental Mutation 'R1695:Pcdh1'
ID 192173
Institutional Source Beutler Lab
Gene Symbol Pcdh1
Ensembl Gene ENSMUSG00000051375
Gene Name protocadherin 1
Synonyms 2010005A06Rik
MMRRC Submission 039728-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.365) question?
Stock # R1695 (G1)
Quality Score 225
Status Not validated
Chromosome 18
Chromosomal Location 38318967-38345023 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 38335921 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Histidine at position 238 (R238H)
Ref Sequence ENSEMBL: ENSMUSP00000124732 (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: R238H

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000055199
Gene: ENSMUSG00000051375
AA Change: R238H

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: R238H

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000125309
Gene: ENSMUSG00000051375
AA Change: R238H

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: ENSMUST00000160721
AA Change: R238H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000124732
Gene: ENSMUSG00000051375
AA Change: R238H

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: R99H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: R99H

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: 99.1%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 93.2%
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: 83 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam1b T A 5: 121,638,970 (GRCm39) T692S probably benign Het
Adgrf3 T A 5: 30,408,553 (GRCm39) N75I probably benign Het
Adgrg5 A G 8: 95,664,373 (GRCm39) M328V probably damaging Het
Adk A G 14: 21,431,668 (GRCm39) D286G probably benign Het
Ankrd28 T A 14: 31,429,201 (GRCm39) D917V probably damaging Het
Appl2 C T 10: 83,457,446 (GRCm39) D141N probably damaging Het
Arfgef2 T C 2: 166,706,632 (GRCm39) V952A probably damaging Het
Arpc2 T A 1: 74,287,391 (GRCm39) H70Q probably damaging Het
Bpifa5 T C 2: 154,009,580 (GRCm39) L261P probably damaging Het
Brca1 G T 11: 101,415,281 (GRCm39) T951K probably damaging Het
Ccdc73 A T 2: 104,822,450 (GRCm39) S800C probably damaging Het
Cdh15 C G 8: 123,588,755 (GRCm39) D276E probably benign Het
Cfap119 A G 7: 127,186,745 (GRCm39) probably null Het
Cfap418 T A 4: 10,874,644 (GRCm39) D10E probably damaging Het
Cfh T C 1: 140,030,575 (GRCm39) I551V probably damaging Het
Chd7 T A 4: 8,833,960 (GRCm39) L1238Q probably damaging Het
Chd9 T G 8: 91,728,410 (GRCm39) F1275L probably damaging Het
Chrnb3 A G 8: 27,883,728 (GRCm39) Y155C probably damaging Het
Cltc C A 11: 86,591,886 (GRCm39) probably null Het
Ctsll3 T A 13: 60,948,791 (GRCm39) N55Y probably damaging Het
Cysltr2 T C 14: 73,267,321 (GRCm39) M130V probably benign Het
Daglb T C 5: 143,480,361 (GRCm39) M455T probably benign Het
Dbn1 A G 13: 55,624,521 (GRCm39) S343P probably benign Het
Dnah2 T A 11: 69,405,517 (GRCm39) D665V possibly damaging Het
Dusp6 T A 10: 99,099,555 (GRCm39) M1K probably null Het
Eif3m T C 2: 104,847,298 (GRCm39) E12G probably damaging Het
Epha2 T C 4: 141,033,828 (GRCm39) V29A possibly damaging Het
Farp2 T A 1: 93,488,047 (GRCm39) N91K probably damaging Het
Ferd3l C A 12: 33,978,971 (GRCm39) S161R probably benign Het
Fgd2 A T 17: 29,587,219 (GRCm39) D315V possibly damaging Het
Fhip2a T C 19: 57,367,603 (GRCm39) W337R probably damaging Het
Fstl4 T A 11: 53,056,705 (GRCm39) probably null Het
Grm5 A G 7: 87,685,311 (GRCm39) D476G possibly damaging Het
Gtf3c3 C T 1: 54,456,937 (GRCm39) A488T probably damaging Het
Hdlbp A G 1: 93,364,922 (GRCm39) L115P probably damaging Het
Hk2 T A 6: 82,721,932 (GRCm39) N136Y probably damaging Het
Hs2st1 G T 3: 144,140,415 (GRCm39) A302E probably benign Het
Htr7 T C 19: 35,947,136 (GRCm39) N293D probably benign Het
Ikbkb T A 8: 23,163,496 (GRCm39) E271D probably benign Het
Il5ra A T 6: 106,715,335 (GRCm39) Y166* probably null Het
Il9r T A 11: 32,143,227 (GRCm39) H244L probably benign Het
Itih4 T C 14: 30,613,456 (GRCm39) probably null Het
Kirrel1 C T 3: 86,996,458 (GRCm39) M380I probably null Het
Large1 A T 8: 73,544,710 (GRCm39) D689E probably damaging Het
Limk2 A G 11: 3,303,275 (GRCm39) probably null Het
Med15 A G 16: 17,540,644 (GRCm39) F34S probably damaging Het
Mprip C T 11: 59,643,357 (GRCm39) T505I probably damaging Het
Mtor T A 4: 148,623,364 (GRCm39) N2071K probably benign Het
Muc16 A G 9: 18,408,729 (GRCm39) L2522P probably damaging Het
Myd88 A T 9: 119,166,908 (GRCm39) probably null Het
Myo7a A C 7: 97,741,703 (GRCm39) F484V possibly damaging Het
Nme1 A C 11: 93,851,593 (GRCm39) L81R probably benign Het
Ntn4 T A 10: 93,569,464 (GRCm39) probably null Het
Or2y13 T C 11: 49,415,162 (GRCm39) V204A probably benign Het
Or4p19 T C 2: 88,242,444 (GRCm39) D186G probably damaging Het
Or51l4 A T 7: 103,404,131 (GRCm39) Y220* probably null Het
Otogl T G 10: 107,649,878 (GRCm39) N1159T probably damaging Het
Pabpc6 G A 17: 9,887,003 (GRCm39) T516I probably benign Het
Pex5l T A 3: 33,008,531 (GRCm39) N151I probably benign Het
Plekha7 T C 7: 115,727,920 (GRCm39) N980S probably damaging Het
Reg4 C T 3: 98,143,677 (GRCm39) T157I probably benign Het
Rev3l A T 10: 39,700,612 (GRCm39) E1703V probably damaging Het
Rev3l G T 10: 39,700,611 (GRCm39) E1703* probably null Het
Rsf1 GCG GCGACG 7: 97,229,114 (GRCm39) probably benign Het
Saal1 T C 7: 46,342,340 (GRCm39) K368E probably damaging Het
Scn9a C T 2: 66,335,220 (GRCm39) W1245* probably null Het
Slc38a11 T A 2: 65,147,315 (GRCm39) L387F probably damaging Het
Sned1 G A 1: 93,209,376 (GRCm39) V830M possibly damaging Het
Sptb C A 12: 76,667,641 (GRCm39) V819L probably benign Het
Sptbn1 T C 11: 30,086,124 (GRCm39) T1195A probably benign Het
Ssna1 C A 2: 25,162,024 (GRCm39) V57F possibly damaging Het
Stk32a G T 18: 43,446,485 (GRCm39) E312* probably null Het
Synpo A G 18: 60,736,459 (GRCm39) F496L probably benign Het
Syt15 C T 14: 33,944,858 (GRCm39) T135M probably benign Het
Tm9sf4 A G 2: 153,032,832 (GRCm39) E246G probably benign Het
Trim44 T C 2: 102,187,830 (GRCm39) M308V possibly damaging Het
Unc119b T A 5: 115,272,885 (GRCm39) K29* probably null Het
Vim T A 2: 13,584,921 (GRCm39) D367E probably benign Het
Virma T A 4: 11,494,814 (GRCm39) N38K probably damaging Het
Vmn1r228 A T 17: 20,996,560 (GRCm39) D319E possibly damaging Het
Vmn2r32 T A 7: 7,466,991 (GRCm39) I846F probably benign Het
Vps13b T C 15: 35,576,667 (GRCm39) V1025A probably benign Het
Vps13c G T 9: 67,879,357 (GRCm39) E566* probably null 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
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
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'- TGGCTCACCCCAACAGGTTAGATG -3'
(R):5'- CGAACTTTGCCTCGCCAGTCATTAC -3'

Sequencing Primer
(F):5'- CCCCAACAGGTTAGATGGAGTG -3'
(R):5'- CAATGGCGTAGCATCCTATGAG -3'
Posted On 2014-05-14