Incidental Mutation 'R7870:Pcdh9'
ID 608067
Institutional Source Beutler Lab
Gene Symbol Pcdh9
Ensembl Gene ENSMUSG00000055421
Gene Name protocadherin 9
Synonyms C630029H24Rik, LOC382930, A730003J17Rik, 1500001L12Rik, C530050I23Rik
MMRRC Submission 045922-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.166) question?
Stock # R7870 (G1)
Quality Score 225.009
Status Not validated
Chromosome 14
Chromosomal Location 93250846-94128115 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 94124693 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 492 (S492R)
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: S492R

PolyPhen 2 Score 0.967 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: S492R

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: ENSMUST00000192221
AA Change: S369R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421
AA Change: S369R

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: S492R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: S492R

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: S492R

PolyPhen 2 Score 0.967 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000141602
Gene: ENSMUSG00000055421
AA Change: S492R

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: S492R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: S492R

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: S492R

PolyPhen 2 Score 0.967 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: S492R

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: 99.7%
  • 20x: 99.0%
Validation Efficiency
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700017N19Rik T A 10: 100,441,505 (GRCm39) F171L probably benign Het
2410137M14Rik A T 17: 37,288,909 (GRCm39) C152S unknown Het
Alb T C 5: 90,620,488 (GRCm39) F533L possibly damaging Het
Alox12b T C 11: 69,060,135 (GRCm39) M616T possibly damaging Het
Atxn2l A G 7: 126,091,924 (GRCm39) F968L probably benign Het
Cadps2 G T 6: 23,263,641 (GRCm39) H1227Q probably benign Het
Cdh18 A T 15: 23,474,413 (GRCm39) D761V possibly damaging Het
Cdkl3 T C 11: 51,909,284 (GRCm39) probably null Het
Chrdl2 T C 7: 99,659,249 (GRCm39) L9P unknown Het
Ctr9 A G 7: 110,651,618 (GRCm39) E946G unknown Het
Cygb T A 11: 116,540,116 (GRCm39) T178S probably benign Het
Cyp2c67 A C 19: 39,597,669 (GRCm39) M443R probably damaging Het
Dnah12 A G 14: 26,578,486 (GRCm39) T3082A probably benign Het
Flnc C T 6: 29,454,306 (GRCm39) T1906I probably damaging Het
Gm14496 A G 2: 181,637,906 (GRCm39) I327V probably benign Het
Gm29106 T A 1: 118,126,885 (GRCm39) N192K possibly damaging Het
H3f3a A T 1: 180,639,490 (GRCm39) M1K probably null Het
Htt T A 5: 35,055,891 (GRCm39) W2601R possibly damaging Het
Il18r1 T A 1: 40,530,296 (GRCm39) I341K probably benign Het
Kcnj1 G A 9: 32,307,881 (GRCm39) V102I probably benign Het
Lrp3 C A 7: 34,910,922 (GRCm39) G41V probably damaging Het
Lrrc9 G T 12: 72,532,964 (GRCm39) K944N probably damaging Het
Mettl21e T A 1: 44,249,371 (GRCm39) E95V probably damaging Het
Mib1 G A 18: 10,798,446 (GRCm39) R769Q possibly damaging Het
Myh7 C G 14: 55,226,258 (GRCm39) D461H probably damaging Het
Mymk A G 2: 26,952,298 (GRCm39) S190P probably damaging Het
Neb G A 2: 52,215,761 (GRCm39) P182L probably damaging Het
Nfil3 A G 13: 53,122,449 (GRCm39) Y152H probably damaging Het
Nisch A G 14: 30,894,052 (GRCm39) Y1174H probably damaging Het
Nyap1 G C 5: 137,733,658 (GRCm39) Y458* probably null Het
Or4d5 A C 9: 40,011,973 (GRCm39) V271G possibly damaging Het
Or52z13 T A 7: 103,247,473 (GRCm39) C317S probably damaging Het
Or5h17 G A 16: 58,820,086 (GRCm39) V13I probably benign Het
Pars2 T A 4: 106,511,276 (GRCm39) Y353N probably damaging Het
Patj G T 4: 98,312,553 (GRCm39) G297V probably damaging Het
Pcyox1 G A 6: 86,369,323 (GRCm39) R168C probably damaging Het
Plbd1 A T 6: 136,594,326 (GRCm39) Y308N possibly damaging Het
Rax A G 18: 66,071,284 (GRCm39) V117A probably benign Het
Rdh9 C A 10: 127,612,566 (GRCm39) N71K probably benign Het
Sap130 A G 18: 31,853,714 (GRCm39) N968S probably benign Het
Sema5a A T 15: 32,609,485 (GRCm39) I464F probably benign Het
Sez6l T G 5: 112,586,447 (GRCm39) D683A probably damaging Het
Slit2 C A 5: 48,459,649 (GRCm39) P1310T probably damaging Het
Snap47 T C 11: 59,328,904 (GRCm39) M133V probably benign Het
Son TACCATGGACTCCCAGATGTTAGCCTCTAGCACCATGGACTCCCAGATGTTAGCCTCTAGCACCATGGACTCCCAGATGTTAGCAACTAGCACCATGGACTCCCAGATGTTAGC TACCATGGACTCCCAGATGTTAGCCTCTAGCACCATGGACTCCCAGATGTTAGCAACTAGCACCATGGACTCCCAGATGTTAGC 16: 91,453,486 (GRCm39) probably benign Het
Srcap G A 7: 127,159,730 (GRCm39) S3202N unknown Het
Ssh2 T C 11: 77,344,441 (GRCm39) W809R probably benign Het
Stau1 G T 2: 166,792,870 (GRCm39) A365D possibly damaging Het
Tfpi2 A G 6: 3,968,281 (GRCm39) L15P probably damaging Het
Thbs1 A T 2: 117,945,508 (GRCm39) N329I possibly damaging Het
Tmem65 A T 15: 58,659,010 (GRCm39) D184E probably damaging Het
Trpm6 G T 19: 18,792,605 (GRCm39) E676D probably benign Het
Vdr T G 15: 97,782,771 (GRCm39) D17A possibly damaging Het
Vmn1r123 C T 7: 20,896,192 (GRCm39) T28I probably damaging Het
Wdr90 A G 17: 26,079,513 (GRCm39) L207P probably damaging Het
Zfp354c TGTCACACTCG TG 11: 50,706,065 (GRCm39) probably benign Het
Zfp598 A G 17: 24,898,304 (GRCm39) E402G probably damaging Het
Other mutations in Pcdh9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00482:Pcdh9 APN 14 93,564,130 (GRCm39) missense probably damaging 1.00
IGL02183:Pcdh9 APN 14 94,123,720 (GRCm39) missense probably benign 0.01
IGL02244:Pcdh9 APN 14 93,564,204 (GRCm39) missense probably damaging 1.00
IGL02571:Pcdh9 APN 14 93,798,023 (GRCm39) splice site probably benign
IGL03018:Pcdh9 APN 14 93,253,012 (GRCm39) missense probably null
I1329:Pcdh9 UTSW 14 94,123,645 (GRCm39) missense probably benign 0.00
R0027:Pcdh9 UTSW 14 94,126,081 (GRCm39) missense probably null 0.99
R0027:Pcdh9 UTSW 14 94,126,081 (GRCm39) missense probably null 0.99
R0477:Pcdh9 UTSW 14 94,125,114 (GRCm39) missense probably damaging 0.99
R0499:Pcdh9 UTSW 14 94,123,671 (GRCm39) missense probably damaging 1.00
R0787:Pcdh9 UTSW 14 94,124,193 (GRCm39) missense possibly damaging 0.88
R1205:Pcdh9 UTSW 14 94,123,501 (GRCm39) missense probably benign 0.01
R1616:Pcdh9 UTSW 14 94,124,405 (GRCm39) nonsense probably null
R1620:Pcdh9 UTSW 14 94,125,741 (GRCm39) missense probably damaging 1.00
R1622:Pcdh9 UTSW 14 94,123,311 (GRCm39) missense probably benign 0.03
R1708:Pcdh9 UTSW 14 94,125,741 (GRCm39) missense probably damaging 1.00
R1721:Pcdh9 UTSW 14 94,125,471 (GRCm39) missense probably damaging 1.00
R1753:Pcdh9 UTSW 14 94,124,661 (GRCm39) missense probably benign 0.33
R1799:Pcdh9 UTSW 14 94,126,107 (GRCm39) missense probably benign 0.36
R1867:Pcdh9 UTSW 14 94,125,471 (GRCm39) missense probably damaging 1.00
R1987:Pcdh9 UTSW 14 94,125,741 (GRCm39) missense probably damaging 1.00
R1988:Pcdh9 UTSW 14 94,125,741 (GRCm39) missense probably damaging 1.00
R2444:Pcdh9 UTSW 14 94,124,227 (GRCm39) missense probably benign 0.10
R3895:Pcdh9 UTSW 14 94,124,974 (GRCm39) missense probably damaging 1.00
R3926:Pcdh9 UTSW 14 94,124,246 (GRCm39) nonsense probably null
R4166:Pcdh9 UTSW 14 94,124,956 (GRCm39) nonsense probably null
R4429:Pcdh9 UTSW 14 94,124,820 (GRCm39) missense probably damaging 0.96
R4589:Pcdh9 UTSW 14 94,125,628 (GRCm39) missense probably damaging 1.00
R4604:Pcdh9 UTSW 14 94,124,616 (GRCm39) missense probably damaging 1.00
R4607:Pcdh9 UTSW 14 93,253,009 (GRCm39) missense probably benign 0.08
R4621:Pcdh9 UTSW 14 94,125,079 (GRCm39) missense probably benign 0.12
R4624:Pcdh9 UTSW 14 94,123,845 (GRCm39) missense probably damaging 1.00
R4712:Pcdh9 UTSW 14 94,126,067 (GRCm39) missense probably damaging 1.00
R4788:Pcdh9 UTSW 14 94,124,851 (GRCm39) missense probably damaging 1.00
R4831:Pcdh9 UTSW 14 94,125,377 (GRCm39) missense probably damaging 1.00
R4883:Pcdh9 UTSW 14 94,126,164 (GRCm39) missense possibly damaging 0.83
R5034:Pcdh9 UTSW 14 93,564,285 (GRCm39) missense probably benign 0.13
R5175:Pcdh9 UTSW 14 94,125,879 (GRCm39) missense probably damaging 1.00
R5637:Pcdh9 UTSW 14 94,123,198 (GRCm39) missense possibly damaging 0.91
R5743:Pcdh9 UTSW 14 94,124,160 (GRCm39) missense probably damaging 1.00
R5753:Pcdh9 UTSW 14 94,125,597 (GRCm39) missense probably damaging 1.00
R5770:Pcdh9 UTSW 14 94,124,379 (GRCm39) missense probably damaging 1.00
R5900:Pcdh9 UTSW 14 93,564,156 (GRCm39) missense probably damaging 0.98
R5986:Pcdh9 UTSW 14 94,124,484 (GRCm39) missense probably damaging 1.00
R6052:Pcdh9 UTSW 14 94,123,282 (GRCm39) missense probably benign 0.40
R6113:Pcdh9 UTSW 14 94,124,544 (GRCm39) missense probably damaging 1.00
R6223:Pcdh9 UTSW 14 93,253,169 (GRCm39) missense probably benign 0.18
R6415:Pcdh9 UTSW 14 93,253,278 (GRCm39) missense possibly damaging 0.83
R6435:Pcdh9 UTSW 14 94,125,280 (GRCm39) missense probably benign 0.01
R7064:Pcdh9 UTSW 14 94,123,585 (GRCm39) missense probably damaging 1.00
R7143:Pcdh9 UTSW 14 94,125,708 (GRCm39) missense probably damaging 0.99
R7219:Pcdh9 UTSW 14 93,253,216 (GRCm39) missense possibly damaging 0.87
R7262:Pcdh9 UTSW 14 93,253,141 (GRCm39) missense probably benign 0.01
R7354:Pcdh9 UTSW 14 94,125,706 (GRCm39) missense probably benign 0.28
R7369:Pcdh9 UTSW 14 94,123,803 (GRCm39) missense possibly damaging 0.67
R7427:Pcdh9 UTSW 14 94,124,547 (GRCm39) missense probably damaging 1.00
R7428:Pcdh9 UTSW 14 94,124,547 (GRCm39) missense probably damaging 1.00
R7780:Pcdh9 UTSW 14 94,123,987 (GRCm39) missense possibly damaging 0.91
R7921:Pcdh9 UTSW 14 93,253,001 (GRCm39) missense probably benign
R8052:Pcdh9 UTSW 14 94,123,222 (GRCm39) missense probably benign 0.00
R8252:Pcdh9 UTSW 14 94,126,086 (GRCm39) missense probably damaging 1.00
R8671:Pcdh9 UTSW 14 94,126,086 (GRCm39) missense probably damaging 1.00
R8672:Pcdh9 UTSW 14 94,124,529 (GRCm39) missense probably benign 0.08
R8724:Pcdh9 UTSW 14 94,124,583 (GRCm39) missense probably benign 0.19
R8974:Pcdh9 UTSW 14 94,125,113 (GRCm39) missense probably benign 0.20
R9044:Pcdh9 UTSW 14 94,124,247 (GRCm39) missense probably damaging 1.00
R9486:Pcdh9 UTSW 14 93,797,956 (GRCm39) missense possibly damaging 0.73
R9534:Pcdh9 UTSW 14 94,123,656 (GRCm39) missense probably damaging 0.99
X0012:Pcdh9 UTSW 14 94,124,080 (GRCm39) missense possibly damaging 0.71
X0067:Pcdh9 UTSW 14 93,564,285 (GRCm39) missense probably benign 0.13
Predicted Primers PCR Primer
(F):5'- AACTATCACTGCTGCTTGGCTC -3'
(R):5'- TCTCTGCTGGACTATGAGGG -3'

Sequencing Primer
(F):5'- ACTGCTGCTTGGCTCTGGAG -3'
(R):5'- GCACCAAAGAATTCAGCTTTAAAATC -3'
Posted On 2019-12-20