Incidental Mutation 'R8671:Pcdh9'
ID 661178
Institutional Source Beutler Lab
Gene Symbol Pcdh9
Ensembl Gene ENSMUSG00000055421
Gene Name protocadherin 9
Synonyms C630029H24Rik, A730003J17Rik, C530050I23Rik, LOC382930, 1500001L12Rik
MMRRC Submission 068526-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.173) question?
Stock # R8671 (G1)
Quality Score 225.009
Status Validated
Chromosome 14
Chromosomal Location 93013410-93890679 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to C at 93888650 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 28 (Y28C)
Ref Sequence ENSEMBL: ENSMUSP00000070935 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000068992] [ENSMUST00000192221] [ENSMUST00000193901] [ENSMUST00000194056] [ENSMUST00000195376] [ENSMUST00000195826]
AlphaFold F8VPK8
Predicted Effect probably damaging
Transcript: ENSMUST00000068992
AA Change: Y28C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: Y28C

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 8.37e-3 SMART
CA 164 250 1.01e-20 SMART
CA 274 356 2.34e-25 SMART
CA 386 467 2.14e-19 SMART
CA 491 570 4.27e-28 SMART
CA 594 673 2.45e-28 SMART
CA 700 782 1.01e-6 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 858 883 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000192221
SMART Domains Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421

DomainStartEndE-ValueType
CA 41 127 1.01e-20 SMART
CA 151 233 2.34e-25 SMART
CA 263 344 2.14e-19 SMART
CA 368 447 4.27e-28 SMART
CA 471 550 2.45e-28 SMART
CA 577 659 1.01e-6 SMART
transmembrane domain 691 713 N/A INTRINSIC
low complexity region 735 760 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000193901
AA Change: Y28C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: Y28C

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 8.37e-3 SMART
CA 164 250 1.01e-20 SMART
CA 274 356 2.34e-25 SMART
CA 386 467 2.14e-19 SMART
CA 491 570 4.27e-28 SMART
CA 594 673 2.45e-28 SMART
CA 700 782 1.01e-6 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 858 883 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000194056
AA Change: Y28C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141602
Gene: ENSMUSG00000055421
AA Change: Y28C

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 4.1e-5 SMART
CA 164 250 4.8e-23 SMART
CA 274 356 1.2e-27 SMART
CA 386 467 1.1e-21 SMART
CA 491 570 2e-30 SMART
CA 594 673 1.2e-30 SMART
CA 700 782 4.9e-9 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 860 873 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000194129
Predicted Effect probably damaging
Transcript: ENSMUST00000195376
AA Change: Y28C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: Y28C

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 4.1e-5 SMART
CA 164 250 4.8e-23 SMART
CA 274 356 1.2e-27 SMART
CA 386 467 1.1e-21 SMART
CA 491 570 2e-30 SMART
CA 594 673 1.2e-30 SMART
CA 700 782 4.9e-9 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 858 883 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000195826
AA Change: Y28C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: Y28C

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 8.37e-3 SMART
CA 164 250 1.01e-20 SMART
CA 274 356 2.34e-25 SMART
CA 386 467 2.14e-19 SMART
CA 491 570 4.27e-28 SMART
CA 594 673 2.45e-28 SMART
CA 700 782 1.01e-6 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 858 883 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
Validation Efficiency 100% (48/48)
MGI Phenotype FUNCTION: This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2012]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired long-term social and bject recognition and sensorimotor development. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310002L09Rik C T 4: 73,942,929 (GRCm38) E145K probably damaging Het
4930430A15Rik T C 2: 111,229,532 (GRCm38) probably benign Het
4930467E23Rik T A 8: 19,734,759 (GRCm38) L203* probably null Het
Ambp A T 4: 63,150,419 (GRCm38) Y120* probably null Het
Ankrd36 C T 11: 5,629,312 (GRCm38) A192V probably benign Het
Apol7e A T 15: 77,717,603 (GRCm38) M134L probably benign Het
Atg9b A T 5: 24,386,109 (GRCm38) N774K probably benign Het
BC027072 G T 17: 71,751,377 (GRCm38) A435E probably benign Het
Catsperb T A 12: 101,594,337 (GRCm38) N862K possibly damaging Het
Ccdc7a T A 8: 128,920,467 (GRCm38) D648V probably damaging Het
Cfap54 G T 10: 92,955,072 (GRCm38) P1855T unknown Het
Clcnkb T A 4: 141,412,230 (GRCm38) T154S probably damaging Het
Cux1 C T 5: 136,250,600 (GRCm38) R609H probably damaging Het
Eif2ak4 A G 2: 118,422,186 (GRCm38) D413G possibly damaging Het
Flnc T C 6: 29,443,502 (GRCm38) probably null Het
Grm5 T C 7: 88,116,290 (GRCm38) probably null Het
Hectd3 T G 4: 116,996,581 (GRCm38) F225V possibly damaging Het
Hpcal4 G T 4: 123,189,183 (GRCm38) M107I probably benign Het
Idh2 TCCCAGG T 7: 80,098,331 (GRCm38) probably benign Het
Ikbkap A G 4: 56,771,453 (GRCm38) L948P probably damaging Het
Larp4 C A 15: 100,010,458 (GRCm38) Q607K probably benign Het
March8 A G 6: 116,401,854 (GRCm38) R250G probably benign Het
Med13 A C 11: 86,271,097 (GRCm38) N2135K probably damaging Het
Msh5 T A 17: 35,045,933 (GRCm38) R89* probably null Het
Musk T G 4: 58,286,051 (GRCm38) probably benign Het
Myo18b T C 5: 112,874,743 (GRCm38) Q261R unknown Het
Npr1 A T 3: 90,456,157 (GRCm38) probably benign Het
Nynrin T A 14: 55,870,442 (GRCm38) V1002E possibly damaging Het
Olfr1138 A T 2: 87,737,646 (GRCm38) L226Q probably damaging Het
Olfr1195 A T 2: 88,683,105 (GRCm38) F209Y probably benign Het
Olfr1315-ps1 T A 2: 112,110,988 (GRCm38) K88M probably damaging Het
Olfr167 T C 16: 19,515,054 (GRCm38) Y194C possibly damaging Het
Pmpca G C 2: 26,395,034 (GRCm38) E424Q possibly damaging Het
Prkd1 T A 12: 50,388,408 (GRCm38) N512I probably benign Het
Pwwp2b C T 7: 139,256,410 (GRCm38) P589L probably damaging Het
Rasgrp4 G A 7: 29,143,027 (GRCm38) G242D probably damaging Het
Rcbtb1 T G 14: 59,230,524 (GRCm38) V480G probably damaging Het
Rptn A G 3: 93,398,194 (GRCm38) S945G probably benign Het
Slc22a2 C T 17: 12,605,976 (GRCm38) Q242* probably null Het
Slfn3 T A 11: 83,212,999 (GRCm38) V232E probably benign Het
Stab1 T A 14: 31,157,408 (GRCm38) K705M probably damaging Het
Syn2 C A 6: 115,278,167 (GRCm38) S480* probably null Het
Thsd4 A T 9: 60,394,445 (GRCm38) L189H probably damaging Het
Tinagl1 T C 4: 130,167,804 (GRCm38) T250A probably benign Het
Tnc A T 4: 64,017,446 (GRCm38) C418S probably damaging Het
Ube2q1 A G 3: 89,776,078 (GRCm38) E110G probably damaging Het
Wdfy4 G T 14: 32,971,765 (GRCm38) probably benign Het
Xcl1 T C 1: 164,931,850 (GRCm38) M94V probably benign Het
Zfp369 T C 13: 65,296,281 (GRCm38) S413P possibly damaging Het
Zfp454 A C 11: 50,873,768 (GRCm38) I279S possibly damaging Het
Zfp971 A C 2: 178,033,937 (GRCm38) Q443P probably damaging Het
Other mutations in Pcdh9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00482:Pcdh9 APN 14 93,326,694 (GRCm38) missense probably damaging 1.00
IGL02183:Pcdh9 APN 14 93,886,284 (GRCm38) missense probably benign 0.01
IGL02244:Pcdh9 APN 14 93,326,768 (GRCm38) missense probably damaging 1.00
IGL02571:Pcdh9 APN 14 93,560,587 (GRCm38) splice site probably benign
IGL03018:Pcdh9 APN 14 93,015,576 (GRCm38) missense probably null
I1329:Pcdh9 UTSW 14 93,886,209 (GRCm38) missense probably benign 0.00
R0027:Pcdh9 UTSW 14 93,888,645 (GRCm38) missense probably null 0.99
R0027:Pcdh9 UTSW 14 93,888,645 (GRCm38) missense probably null 0.99
R0477:Pcdh9 UTSW 14 93,887,678 (GRCm38) missense probably damaging 0.99
R0499:Pcdh9 UTSW 14 93,886,235 (GRCm38) missense probably damaging 1.00
R0787:Pcdh9 UTSW 14 93,886,757 (GRCm38) missense possibly damaging 0.88
R1205:Pcdh9 UTSW 14 93,886,065 (GRCm38) missense probably benign 0.01
R1616:Pcdh9 UTSW 14 93,886,969 (GRCm38) nonsense probably null
R1620:Pcdh9 UTSW 14 93,888,305 (GRCm38) missense probably damaging 1.00
R1622:Pcdh9 UTSW 14 93,885,875 (GRCm38) missense probably benign 0.03
R1708:Pcdh9 UTSW 14 93,888,305 (GRCm38) missense probably damaging 1.00
R1721:Pcdh9 UTSW 14 93,888,035 (GRCm38) missense probably damaging 1.00
R1753:Pcdh9 UTSW 14 93,887,225 (GRCm38) missense probably benign 0.33
R1799:Pcdh9 UTSW 14 93,888,671 (GRCm38) missense probably benign 0.36
R1867:Pcdh9 UTSW 14 93,888,035 (GRCm38) missense probably damaging 1.00
R1987:Pcdh9 UTSW 14 93,888,305 (GRCm38) missense probably damaging 1.00
R1988:Pcdh9 UTSW 14 93,888,305 (GRCm38) missense probably damaging 1.00
R2444:Pcdh9 UTSW 14 93,886,791 (GRCm38) missense probably benign 0.10
R3895:Pcdh9 UTSW 14 93,887,538 (GRCm38) missense probably damaging 1.00
R3926:Pcdh9 UTSW 14 93,886,810 (GRCm38) nonsense probably null
R4166:Pcdh9 UTSW 14 93,887,520 (GRCm38) nonsense probably null
R4429:Pcdh9 UTSW 14 93,887,384 (GRCm38) missense probably damaging 0.96
R4589:Pcdh9 UTSW 14 93,888,192 (GRCm38) missense probably damaging 1.00
R4604:Pcdh9 UTSW 14 93,887,180 (GRCm38) missense probably damaging 1.00
R4607:Pcdh9 UTSW 14 93,015,573 (GRCm38) missense probably benign 0.08
R4621:Pcdh9 UTSW 14 93,887,643 (GRCm38) missense probably benign 0.12
R4624:Pcdh9 UTSW 14 93,886,409 (GRCm38) missense probably damaging 1.00
R4712:Pcdh9 UTSW 14 93,888,631 (GRCm38) missense probably damaging 1.00
R4788:Pcdh9 UTSW 14 93,887,415 (GRCm38) missense probably damaging 1.00
R4831:Pcdh9 UTSW 14 93,887,941 (GRCm38) missense probably damaging 1.00
R4883:Pcdh9 UTSW 14 93,888,728 (GRCm38) missense possibly damaging 0.83
R5034:Pcdh9 UTSW 14 93,326,849 (GRCm38) missense probably benign 0.13
R5175:Pcdh9 UTSW 14 93,888,443 (GRCm38) missense probably damaging 1.00
R5637:Pcdh9 UTSW 14 93,885,762 (GRCm38) missense possibly damaging 0.91
R5743:Pcdh9 UTSW 14 93,886,724 (GRCm38) missense probably damaging 1.00
R5753:Pcdh9 UTSW 14 93,888,161 (GRCm38) missense probably damaging 1.00
R5770:Pcdh9 UTSW 14 93,886,943 (GRCm38) missense probably damaging 1.00
R5900:Pcdh9 UTSW 14 93,326,720 (GRCm38) missense probably damaging 0.98
R5986:Pcdh9 UTSW 14 93,887,048 (GRCm38) missense probably damaging 1.00
R6052:Pcdh9 UTSW 14 93,885,846 (GRCm38) missense probably benign 0.40
R6113:Pcdh9 UTSW 14 93,887,108 (GRCm38) missense probably damaging 1.00
R6223:Pcdh9 UTSW 14 93,015,733 (GRCm38) missense probably benign 0.18
R6415:Pcdh9 UTSW 14 93,015,842 (GRCm38) missense possibly damaging 0.83
R6435:Pcdh9 UTSW 14 93,887,844 (GRCm38) missense probably benign 0.01
R7064:Pcdh9 UTSW 14 93,886,149 (GRCm38) missense probably damaging 1.00
R7143:Pcdh9 UTSW 14 93,888,272 (GRCm38) missense probably damaging 0.99
R7219:Pcdh9 UTSW 14 93,015,780 (GRCm38) missense possibly damaging 0.87
R7262:Pcdh9 UTSW 14 93,015,705 (GRCm38) missense probably benign 0.01
R7354:Pcdh9 UTSW 14 93,888,270 (GRCm38) missense probably benign 0.28
R7369:Pcdh9 UTSW 14 93,886,367 (GRCm38) missense possibly damaging 0.67
R7427:Pcdh9 UTSW 14 93,887,111 (GRCm38) missense probably damaging 1.00
R7428:Pcdh9 UTSW 14 93,887,111 (GRCm38) missense probably damaging 1.00
R7780:Pcdh9 UTSW 14 93,886,551 (GRCm38) missense possibly damaging 0.91
R7870:Pcdh9 UTSW 14 93,887,257 (GRCm38) missense probably damaging 0.97
R7921:Pcdh9 UTSW 14 93,015,565 (GRCm38) missense probably benign
R8052:Pcdh9 UTSW 14 93,885,786 (GRCm38) missense probably benign 0.00
R8252:Pcdh9 UTSW 14 93,888,650 (GRCm38) missense probably damaging 1.00
R8672:Pcdh9 UTSW 14 93,887,093 (GRCm38) missense probably benign 0.08
R8724:Pcdh9 UTSW 14 93,887,147 (GRCm38) missense probably benign 0.19
R8974:Pcdh9 UTSW 14 93,887,677 (GRCm38) missense probably benign 0.20
R9044:Pcdh9 UTSW 14 93,886,811 (GRCm38) missense probably damaging 1.00
R9486:Pcdh9 UTSW 14 93,560,520 (GRCm38) missense possibly damaging 0.73
R9534:Pcdh9 UTSW 14 93,886,220 (GRCm38) missense probably damaging 0.99
X0012:Pcdh9 UTSW 14 93,886,644 (GRCm38) missense possibly damaging 0.71
X0067:Pcdh9 UTSW 14 93,326,849 (GRCm38) missense probably benign 0.13
Predicted Primers PCR Primer
(F):5'- TCCCCAGTGCTACTCGATAC -3'
(R):5'- GCTGTCTCCACATAAGAGATGAG -3'

Sequencing Primer
(F):5'- TACTCGATACTTTCACCAGAGGGG -3'
(R):5'- GAGATGAGATGTAATGCCTCCTCC -3'
Posted On 2021-03-08